diff --git a/converter-CellDesigner/.settings/org.eclipse.wst.common.component b/converter-CellDesigner/.settings/org.eclipse.wst.common.component
index 547a0c08e066ce2bbb19695db30871b995ff9509..a38de8eadd1789aa27804b0c552b62d553399fe4 100644
--- a/converter-CellDesigner/.settings/org.eclipse.wst.common.component
+++ b/converter-CellDesigner/.settings/org.eclipse.wst.common.component
@@ -1,5 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?><project-modules id="moduleCoreId" project-version="1.5.0">
<wb-module deploy-name="MapViewer-converter-CellDesigner">
<wb-resource deploy-path="/" source-path="/src/main/java"/>
+ <wb-resource deploy-path="/" source-path="/src/main/resources"/>
</wb-module>
</project-modules>
diff --git a/converter-CellDesigner/pom.xml b/converter-CellDesigner/pom.xml
index f21898b074dcfa49da8fa7073d7e3e95732a85ac..e6b82360bbd595417f95a43183a8a5c019b66ed6 100644
--- a/converter-CellDesigner/pom.xml
+++ b/converter-CellDesigner/pom.xml
@@ -1,45 +1,45 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>parent</artifactId>
- <version>1.0</version>
- </parent>
- <artifactId>converter-CellDesigner</artifactId>
- <name>CellDesigner converter</name>
- <description>CellDesigner converter for model</description>
-
- <dependencies>
-
- <!-- dependency from the MapViewer model -->
-
- <dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>model</artifactId>
- <version>1.0</version>
- </dependency>
-
- <dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>converter</artifactId>
- <version>1.0</version>
- </dependency>
-
- <!-- Log4J -->
- <dependency>
- <groupId>log4j</groupId>
- <artifactId>log4j</artifactId>
- <version>${log4j.version}</version>
- </dependency>
-
-<!-- mockito used for testing -->
- <dependency>
- <groupId>org.mockito</groupId>
- <artifactId>mockito-all</artifactId>
- <version>${mockito.version}</version>
- <scope>test</scope>
- </dependency>
-
- </dependencies>
-
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>parent</artifactId>
+ <version>1.0</version>
+ </parent>
+ <artifactId>converter-CellDesigner</artifactId>
+ <name>CellDesigner converter</name>
+ <description>CellDesigner converter for model</description>
+
+ <dependencies>
+
+ <!-- dependency from the MapViewer model -->
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>model</artifactId>
+ <version>1.0</version>
+ </dependency>
+
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>converter</artifactId>
+ <version>1.0</version>
+ </dependency>
+
+ <!-- Log4J -->
+ <dependency>
+ <groupId>log4j</groupId>
+ <artifactId>log4j</artifactId>
+ <version>${log4j.version}</version>
+ </dependency>
+
+ <!-- mockito used for testing -->
+ <dependency>
+ <groupId>org.mockito</groupId>
+ <artifactId>mockito-all</artifactId>
+ <version>${mockito.version}</version>
+ <scope>test</scope>
+ </dependency>
+
+ </dependencies>
+
</project>
\ No newline at end of file
diff --git a/converter-sbml/.classpath b/converter-sbml/.classpath
new file mode 100644
index 0000000000000000000000000000000000000000..121fc2c8190e91386cecbac241fc4a0b7e6bb5ad
--- /dev/null
+++ b/converter-sbml/.classpath
@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="src" output="target/classes" path="src/main/java">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="src" output="target/test-classes" path="src/test/java">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="output" path="target/classes"/>
+</classpath>
diff --git a/converter-sbml/.project b/converter-sbml/.project
new file mode 100644
index 0000000000000000000000000000000000000000..0a5695c6c29ccbc08e4825dbbe3b8aa759daa0f0
--- /dev/null
+++ b/converter-sbml/.project
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+ <name>converter-sbml</name>
+ <comment></comment>
+ <projects>
+ </projects>
+ <buildSpec>
+ <buildCommand>
+ <name>org.eclipse.jdt.core.javabuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+ <name>org.eclipse.m2e.core.maven2Builder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ </buildSpec>
+ <natures>
+ <nature>org.eclipse.jdt.core.javanature</nature>
+ <nature>org.eclipse.m2e.core.maven2Nature</nature>
+ </natures>
+</projectDescription>
diff --git a/converter-sbml/.settings/org.eclipse.core.resources.prefs b/converter-sbml/.settings/org.eclipse.core.resources.prefs
new file mode 100644
index 0000000000000000000000000000000000000000..29abf999564110a0d6aca109f55f439c72b7031c
--- /dev/null
+++ b/converter-sbml/.settings/org.eclipse.core.resources.prefs
@@ -0,0 +1,6 @@
+eclipse.preferences.version=1
+encoding//src/main/java=UTF-8
+encoding//src/main/resources=UTF-8
+encoding//src/test/java=UTF-8
+encoding//src/test/resources=UTF-8
+encoding/<project>=UTF-8
diff --git a/converter-sbml/.settings/org.eclipse.jdt.core.prefs b/converter-sbml/.settings/org.eclipse.jdt.core.prefs
new file mode 100644
index 0000000000000000000000000000000000000000..714351aec195a9a572640e6844dcafd51565a2a5
--- /dev/null
+++ b/converter-sbml/.settings/org.eclipse.jdt.core.prefs
@@ -0,0 +1,5 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
+org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.8
diff --git a/converter-sbml/.settings/org.eclipse.m2e.core.prefs b/converter-sbml/.settings/org.eclipse.m2e.core.prefs
new file mode 100644
index 0000000000000000000000000000000000000000..f897a7f1cb2389f85fe6381425d29f0a9866fb65
--- /dev/null
+++ b/converter-sbml/.settings/org.eclipse.m2e.core.prefs
@@ -0,0 +1,4 @@
+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1
diff --git a/converter-sbml/pom.xml b/converter-sbml/pom.xml
new file mode 100644
index 0000000000000000000000000000000000000000..6fc10f0b45cf6f784f66bf45246aa459d1df7c35
--- /dev/null
+++ b/converter-sbml/pom.xml
@@ -0,0 +1,83 @@
+<?xml version="1.0"?>
+<project
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"
+ xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>parent</artifactId>
+ <version>1.0</version>
+ </parent>
+ <artifactId>converter-sbml</artifactId>
+ <name>converter-sbml</name>
+ <url>http://maven.apache.org</url>
+ <properties>
+ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+ </properties>
+
+
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-jar-plugin</artifactId>
+ <version>2.3</version>
+ <configuration>
+ <excludes>
+ <exclude>**/log4j.properties</exclude>
+ </excludes>
+ </configuration>
+ </plugin>
+
+
+ <dependencies>
+
+ <!-- dependency from the minerva model -->
+
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>model</artifactId>
+ <version>1.0</version>
+ </dependency>
+
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>converter</artifactId>
+ <version>1.0</version>
+ </dependency>
+
+ <!-- Log4J -->
+ <dependency>
+ <groupId>log4j</groupId>
+ <artifactId>log4j</artifactId>
+ <version>${log4j.version}</version>
+ </dependency>
+
+ <!-- mockito used for testing -->
+ <dependency>
+ <groupId>org.mockito</groupId>
+ <artifactId>mockito-all</artifactId>
+ <version>${mockito.version}</version>
+ <scope>test</scope>
+ </dependency>
+
+ <dependency>
+ <groupId>org.sbml.jsbml</groupId>
+ <artifactId>jsbml</artifactId>
+ <version>1.2</version>
+ </dependency>
+
+
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>converter-graphics</artifactId>
+ <version>1.0</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>converter-CellDesigner</artifactId>
+ <version>1.0</version>
+ <scope>test</scope>
+ </dependency>
+
+ </dependencies>
+</project>
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentParser.java
new file mode 100644
index 0000000000000000000000000000000000000000..27cc67f3126ab3b670d497aeb02af8bcc2f2a573
--- /dev/null
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentParser.java
@@ -0,0 +1,100 @@
+package lcsb.mapviewer.converter.model.sbml;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import javax.xml.stream.XMLStreamException;
+
+import org.apache.log4j.Logger;
+import org.sbml.jsbml.Annotation;
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.ext.layout.CompartmentGlyph;
+import org.sbml.jsbml.ext.layout.Layout;
+import org.sbml.jsbml.util.NotImplementedException;
+
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
+
+public class SbmlCompartmentParser {
+ Logger logger = Logger.getLogger(SbmlCompartmentParser.class);
+
+ Layout layout;
+
+ public SbmlCompartmentParser(Layout layout) {
+ this.layout = layout;
+ }
+
+ public List<Compartment> parseList(Model sbmlModel) throws InvalidInputDataExecption {
+ List<Compartment> result = new ArrayList<>();
+ for (org.sbml.jsbml.Compartment compartment : sbmlModel.getListOfCompartments()) {
+ result.add(parse(compartment));
+ }
+ if (layout != null) {
+ return mergeLayout(result, layout);
+ } else {
+ return result;
+ }
+ }
+
+ private List<Compartment> mergeLayout(List<Compartment> compartments, Layout sbmlLayout)
+ throws InvalidInputDataExecption {
+ Set<Compartment> used = new HashSet<>();
+ Map<String, Compartment> compartmentById = new HashMap<>();
+ for (Compartment compartment : compartments) {
+ if (compartmentById.get(compartment.getElementId()) != null) {
+ throw new InvalidInputDataExecption("Duplicated element id: " + compartment.getElementId());
+ }
+ compartmentById.put(compartment.getElementId(), compartment);
+ }
+ List<Compartment> result = new ArrayList<>();
+
+ for (CompartmentGlyph glyph : sbmlLayout.getListOfCompartmentGlyphs()) {
+ Compartment source = compartmentById.get(glyph.getCompartment());
+ if (source==null) {
+ throw new InvalidInputDataExecption("Layout contains invalid compartment id: "+glyph.getCompartment());
+ }
+ used.add(source);
+ Compartment compartmentWithLayout = new SquareCompartment(source);
+ compartmentWithLayout.setElementId(glyph.getId());
+ compartmentWithLayout.setX(glyph.getBoundingBox().getPosition().getX());
+ compartmentWithLayout.setY(glyph.getBoundingBox().getPosition().getY());
+ compartmentWithLayout.setWidth(glyph.getBoundingBox().getDimensions().getWidth());
+ compartmentWithLayout.setHeight(glyph.getBoundingBox().getDimensions().getHeight());
+ result.add(compartmentWithLayout);
+ }
+ for (Compartment compartment : compartments) {
+ if (!used.contains(compartment)) {
+ logger.warn("Layout doesn't contain information about compartment: "+compartment.getElementId());
+ result.add(compartment);
+ }
+ }
+ return result;
+ }
+
+ private Compartment parse(org.sbml.jsbml.Compartment compartment) throws InvalidInputDataExecption {
+ Compartment result = new Compartment(compartment.getId());
+ result.setMiriamData(parseAnnotation(compartment.getAnnotation()));
+ result.setName(compartment.getName());
+ try {
+ result.setNotes(compartment.getNotesString());
+ } catch (XMLStreamException e) {
+ throw new InvalidInputDataExecption(compartment.getId() + " Invalid compartment notes", e);
+ }
+ return result;
+ }
+
+ protected Set<MiriamData> parseAnnotation(Annotation annotation) {
+ if (annotation.getCVTermCount() > 0) {
+ throw new NotImplementedException();
+ }
+ Set<MiriamData> result = new HashSet<>();
+ return result;
+ }
+
+}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
new file mode 100644
index 0000000000000000000000000000000000000000..357fcfefaf317e53937a7705f6139107c46efda0
--- /dev/null
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
@@ -0,0 +1,196 @@
+package lcsb.mapviewer.converter.model.sbml;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.Set;
+
+import javax.xml.stream.XMLStreamException;
+
+import org.apache.commons.io.FilenameUtils;
+import org.apache.log4j.Logger;
+import org.sbml.jsbml.SBMLDocument;
+import org.sbml.jsbml.SBMLReader;
+import org.sbml.jsbml.ext.SBasePlugin;
+import org.sbml.jsbml.ext.layout.Layout;
+import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
+import org.sbml.jsbml.util.NotImplementedException;
+
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Element;
+
+public class SbmlParser implements IConverter {
+
+ /**
+ * Default class logger.
+ */
+ Logger logger = Logger.getLogger(SbmlParser.class);
+
+ @Override
+ public Model createModel(ConverterParams params) throws InvalidInputDataExecption {
+ try {
+ Model model = new ModelFullIndexed(null);
+
+ if (params.getFilename() != null) {
+ model.setName(FilenameUtils.getBaseName(params.getFilename()));
+ }
+ SBMLDocument sbmlDocument = SBMLReader.read(params.getInputStream());
+ org.sbml.jsbml.Model sbmlModel = sbmlDocument.getModel();
+ model.setIdModel(sbmlModel.getId());
+
+ Layout layout = getSbmlLayout(sbmlModel);
+
+ SbmlCompartmentParser compartmentParser = new SbmlCompartmentParser(layout);
+
+ Set<MiriamData> annotations = compartmentParser.parseAnnotation(sbmlModel.getAnnotation());
+ if (annotations.size() > 0) {
+ throw new NotImplementedException("Annotations not implemented for model");
+ }
+ model.addElements(compartmentParser.parseList(sbmlModel));
+ if (sbmlModel.getConstraintCount() > 0) {
+ throw new NotImplementedException("Constraints not implemented for model");
+ }
+ if (sbmlModel.getConversionFactorInstance() != null) {
+ throw new NotImplementedException("ConversionFactor not implemented for model");
+ }
+ if (sbmlModel.getCVTermCount() > 0) {
+ throw new NotImplementedException("CVTerms not implemented for model");
+ }
+ if (sbmlModel.getEventCount() > 0) {
+ throw new NotImplementedException("Events not implemented for model");
+ }
+ if (sbmlModel.getEventAssignmentCount() > 0) {
+ throw new NotImplementedException("EventAssignemnts not implemented for model");
+ }
+ if (sbmlModel.getFunctionDefinitionCount() > 0) {
+ throw new NotImplementedException("FunctionDefinition not implemented for model");
+ }
+ if (sbmlModel.getInitialAssignmentCount() > 0) {
+ throw new NotImplementedException("InitialAssignment not implemented for model");
+ }
+ if (sbmlModel.getKineticLawCount() > 0) {
+ throw new NotImplementedException("KineticLaw not implemented for model");
+ }
+ if (sbmlModel.getParameterCount() > 0) {
+ throw new NotImplementedException("Parameter not implemented for model");
+ }
+ if (sbmlModel.getModifierSpeciesReferenceCount() > 0) {
+ throw new NotImplementedException("ModifierSpeciesReference not implemented for model");
+ }
+ if (sbmlModel.getReactionCount() > 0) {
+ throw new NotImplementedException("Reaction not implemented for model");
+ }
+ if (sbmlModel.getRuleCount() > 0) {
+ throw new NotImplementedException("Rule not implemented for model");
+ }
+ if (sbmlModel.getSpeciesCount() > 0) {
+ throw new NotImplementedException("Species not implemented for model");
+ }
+ if (sbmlModel.getSpeciesReferenceCount() > 0) {
+ throw new NotImplementedException("SpeciesReference not implemented for model");
+ }
+ if (sbmlModel.getUnitDefinitionCount() > 0) {
+ logger.warn("Units are not supported");
+ }
+
+ createLayout(model, layout);
+ return model;
+ } catch (XMLStreamException e) {
+ throw new InvalidInputDataExecption(e);
+ }
+ }
+
+ private void createLayout(Model model, Layout layout) {
+ double width;
+ double height;
+ if (layout != null) {
+ width = layout.getDimensions().getWidth();
+ height = layout.getDimensions().getHeight();
+ } else {
+ width = 100;
+ height = 100;
+ double minX = Double.MAX_VALUE;
+ double minY = Double.MAX_VALUE;
+ for (Element element : model.getElements()) {
+ if (element.getX() == null) {
+ throw new NotImplementedException("Element without layout not implemented");
+ }
+ width = Math.max(width, element.getX() + element.getWidth());
+ height = Math.max(height, element.getY() + element.getHeight());
+ minX = Math.min(minX, element.getX());
+ minY = Math.min(minY, element.getY());
+ }
+ if (minX != Double.MAX_VALUE) {
+ minX = Math.max(0, minX);
+ minY = Math.max(0, minY);
+ }
+ width += minX;
+ height += minY;
+ }
+
+ model.setWidth(width);
+ model.setHeight(height);
+ }
+
+ private Layout getSbmlLayout(org.sbml.jsbml.Model sbmlModel) {
+ Layout layout = null;
+ if (sbmlModel.getExtensionCount() > 0) {
+ for (SBasePlugin plugin : sbmlModel.getExtensionPackages().values()) {
+ if (plugin.getClass().equals(org.sbml.jsbml.ext.layout.LayoutModelPlugin.class)) {
+ LayoutModelPlugin layoutPlugin = (LayoutModelPlugin) plugin;
+ if (layoutPlugin.getLayoutCount() == 0) {
+ logger.warn("Layout plugin available but not layouts defined");
+ } else if (layoutPlugin.getLayoutCount() > 1) {
+ logger.warn(layoutPlugin.getLayoutCount() + " layouts defined. Using first one.");
+ layout = layoutPlugin.getLayout(0);
+ } else {
+ layout = layoutPlugin.getLayout(0);
+ }
+ } else {
+ logger.warn("Unknown sbml plugin: " + plugin);
+ }
+ }
+ }
+ return layout;
+ }
+
+ @Override
+ public InputStream exportModelToInputStream(Model model) throws ConverterException, InconsistentModelException {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public File exportModelToFile(Model model, String filePath)
+ throws ConverterException, InconsistentModelException, IOException {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getCommonName() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public MimeType getMimeType() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getFileExtension() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+}
diff --git a/converter-sbml/src/main/resources/log4j.properties b/converter-sbml/src/main/resources/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..a784f69dbe2aa1d6bf3d81fe0083ea25e433fa94
--- /dev/null
+++ b/converter-sbml/src/main/resources/log4j.properties
@@ -0,0 +1,21 @@
+#Set root logger 's level and its appender to an appender called CONSOLE which is defined below.
+log4j.rootLogger=info, SBML_CONSOLE
+
+#Set the behavior of the CONSOLE appender
+log4j.appender.SBML_CONSOLE=org.apache.log4j.ConsoleAppender
+log4j.appender.SBML_CONSOLE.layout=org.apache.log4j.PatternLayout
+log4j.appender.SBML_CONSOLE.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
+#log4j.appender.CONSOLE.layout.ConversionPattern=%m%n
+
+
+#Set the behavior of the FILE appender
+log4j.appender.R=org.apache.log4j.FileAppender
+log4j.appender.R.File=${catalina.home}/logs/MapViewer.log
+log4j.appender.R.layout=org.apache.log4j.PatternLayout
+log4j.appender.R.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
+
+
+log4j.logger.org.springframework=warn
+log4j.logger.org.hibernate=warn
+log4j.logger.lcsb=debug
+log4j.logger.lcsb.mapviewer.common.comparator=info
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..835fe52df8cb3c10948025d3883a51de1c596c3b
--- /dev/null
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java
@@ -0,0 +1,108 @@
+package lcsb.mapviewer.converter.model.sbml;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.PrintWriter;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Collection;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.log4j.Logger;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
+import lcsb.mapviewer.converter.graphics.NormalImageGenerator;
+import lcsb.mapviewer.converter.graphics.PngImageGenerator;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+
+@RunWith(Parameterized.class)
+public class GenericSbmlParserTest {
+
+ static Logger logger = Logger.getLogger(GenericSbmlParserTest.class.getName());
+
+ private Path filePath;
+
+ public GenericSbmlParserTest(Path filePath) {
+ this.filePath = filePath;
+ }
+
+ @Parameters(name = "{index} : {0}")
+ public static Collection<Object[]> data() throws IOException {
+ Collection<Object[]> data = new ArrayList<Object[]>();
+ Files.walk(Paths.get("testFiles/layoutExample")).forEach(fPath -> {
+ if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".xml")) {
+ data.add(new Object[] { fPath });
+ }
+ });
+ return data;
+ }
+
+ @Test
+ public void createModelTest() throws Exception {
+ try {
+ String dir = Files.createTempDirectory("sbgn-temp-images-dir").toFile().getAbsolutePath();
+
+ IConverter converter = new SbmlParser();
+
+ Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
+ model.setName(null);
+
+ Compartment c = new SquareCompartment((Compartment) model.getElements().iterator().next());
+
+ // Create and display image of parsed map
+ AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().height(model.getHeight())
+ .width(model.getWidth()).nested(true).scale(1).level(20).x(0).y(0).model(model);
+ NormalImageGenerator nig = new PngImageGenerator(params);
+ String pathWithouExtension = dir + "/"
+ + filePath.getFileName().toString().substring(0, filePath.getFileName().toString().indexOf(".xml"));
+ String pngFilePath = pathWithouExtension.concat(".png");
+ nig.saveToFile(pngFilePath);
+
+ CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
+ String xmlString = cellDesignerXmlParser.toXml(model);
+
+ String cellDesignerFilePath = pathWithouExtension.concat("_CD.xml");
+ PrintWriter out = new PrintWriter(cellDesignerFilePath);
+ out.print(xmlString);
+ out.close();
+
+ InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
+
+ Model model2 = cellDesignerXmlParser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ AbstractImageGenerator.Params params2 = new AbstractImageGenerator.Params().height(model2.getHeight())
+ .width(model2.getWidth()).nested(true).scale(1).level(20).x(0).y(0).model(model2);
+ NormalImageGenerator nig2 = new PngImageGenerator(params2);
+ String pngFilePath2 = pathWithouExtension.concat("_2.png");
+ nig2.saveToFile(pngFilePath2);
+
+ assertNotNull(model2);
+ ModelComparator comparator = new ModelComparator(1.0);
+ assertEquals(0, comparator.compare(model, model2));
+ FileUtils.deleteDirectory(new File(dir));
+
+ } catch (Exception e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..b0da6b65b91d7c8aada9ef31d8342aa868c2bf50
--- /dev/null
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
@@ -0,0 +1,40 @@
+package lcsb.mapviewer.converter.model.sbml;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.io.FileNotFoundException;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
+
+public class SbmlParserTest {
+ Logger logger = Logger.getLogger(SbmlParserTest.class);
+ SbmlParser parser = new SbmlParser();
+
+ @Test
+ public void testParseCompartment() throws FileNotFoundException, InvalidInputDataExecption {
+ Model model = parser.createModel(
+ new ConverterParams().filename("testFiles/layoutExample/CompartmentGlyph_Example_level2_level3.xml"));
+ assertNotNull(model);
+ assertEquals(1, model.getCompartments().size());
+ Compartment compartment = model.getElementByElementId("CompartmentGlyph_1");
+ assertNotNull(compartment.getX());
+ assertNotNull(compartment.getY());
+ assertTrue(compartment.getWidth()>0);
+ assertTrue(compartment.getHeight()>0);
+ assertNotNull(model.getHeight());
+ assertNotNull(model.getWidth());
+ assertTrue(model.getWidth() >= compartment.getX() + compartment.getWidth());
+ assertTrue(model.getHeight() >= compartment.getY() + compartment.getHeight());
+ assertFalse(compartment.getClass().equals(Compartment.class));
+ }
+
+}
diff --git a/converter-sbml/src/test/resources/log4j.properties b/converter-sbml/src/test/resources/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..a784f69dbe2aa1d6bf3d81fe0083ea25e433fa94
--- /dev/null
+++ b/converter-sbml/src/test/resources/log4j.properties
@@ -0,0 +1,21 @@
+#Set root logger 's level and its appender to an appender called CONSOLE which is defined below.
+log4j.rootLogger=info, SBML_CONSOLE
+
+#Set the behavior of the CONSOLE appender
+log4j.appender.SBML_CONSOLE=org.apache.log4j.ConsoleAppender
+log4j.appender.SBML_CONSOLE.layout=org.apache.log4j.PatternLayout
+log4j.appender.SBML_CONSOLE.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
+#log4j.appender.CONSOLE.layout.ConversionPattern=%m%n
+
+
+#Set the behavior of the FILE appender
+log4j.appender.R=org.apache.log4j.FileAppender
+log4j.appender.R.File=${catalina.home}/logs/MapViewer.log
+log4j.appender.R.layout=org.apache.log4j.PatternLayout
+log4j.appender.R.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
+
+
+log4j.logger.org.springframework=warn
+log4j.logger.org.hibernate=warn
+log4j.logger.lcsb=debug
+log4j.logger.lcsb.mapviewer.common.comparator=info
diff --git a/converter-sbml/testFiles/layoutExample/CompartmentGlyph_Example_level2.xml b/converter-sbml/testFiles/layoutExample/CompartmentGlyph_Example_level2.xml
new file mode 100644
index 0000000000000000000000000000000000000000..b0b7f7067e6e16aa221a9b29cd5326a9747962ae
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/CompartmentGlyph_Example_level2.xml
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+<model id="TestModel_with_modifiers">
+<annotation>
+<listOfLayouts xmlns="http://projects.eml.org/bcb/sbml/level2"
+xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+<layout id="Layout_1">
+<dimensions width="400" height="230"/>
+<listOfCompartmentGlyphs>
+<compartmentGlyph id="CompartmentGlyph_1" compartment="Yeast">
+<boundingBox id="bb1">
+<position x="5" y="5"/>
+<dimensions width="390" height="220"/>
+</boundingBox>
+</compartmentGlyph>
+</listOfCompartmentGlyphs>
+</layout>
+</listOfLayouts>
+</annotation>
+<listOfCompartments>
+<compartment id="Yeast"/>
+</listOfCompartments>
+</model>
+</sbml>
\ No newline at end of file
diff --git a/converter-sbml/testFiles/layoutExample/CompartmentGlyph_Example_level2_level3.xml b/converter-sbml/testFiles/layoutExample/CompartmentGlyph_Example_level2_level3.xml
new file mode 100644
index 0000000000000000000000000000000000000000..d6579fdfb573ab3f992c3ee6aed5121e86b30121
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/CompartmentGlyph_Example_level2_level3.xml
@@ -0,0 +1,33 @@
+<?xml version='1.0' encoding='utf-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" layout:required="false" level="3" version="1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+ <model areaUnits="area" extentUnits="mole" id="TestModel_with_modifiers" lengthUnits="metre" substanceUnits="mole" timeUnits="second" volumeUnits="volume">
+ <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <layout:layout layout:id="Layout_1">
+ <layout:dimensions layout:height="230" layout:width="400" />
+ <layout:listOfCompartmentGlyphs>
+ <layout:compartmentGlyph layout:compartment="Yeast" layout:id="CompartmentGlyph_1">
+ <layout:boundingBox layout:id="bb1">
+ <layout:position layout:x="5" layout:y="5" />
+ <layout:dimensions layout:height="220" layout:width="390" />
+ </layout:boundingBox>
+ </layout:compartmentGlyph>
+ </layout:listOfCompartmentGlyphs>
+ </layout:layout>
+ </layout:listOfLayouts>
+ <listOfUnitDefinitions>
+ <unitDefinition id="volume">
+ <listOfUnits>
+ <unit exponent="1" kind="litre" multiplier="1" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="area">
+ <listOfUnits>
+ <unit exponent="2" kind="metre" multiplier="1" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment constant="true" id="Yeast" spatialDimensions="3" units="volume" />
+ </listOfCompartments>
+ </model>
+</sbml>
diff --git a/converter-sbml/testFiles/layoutExample/CompartmentGlyph_example.xml b/converter-sbml/testFiles/layoutExample/CompartmentGlyph_example.xml
new file mode 100644
index 0000000000000000000000000000000000000000..ed04dd0097a7a1652eaa0fa3030bc0b860e19d82
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/CompartmentGlyph_example.xml
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"
+xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1"
+level="3" version="1" layout:required="false" >
+<model id="TestModel_with_modifiers">
+
+<listOfCompartments>
+<compartment id="Yeast" spatialDimensions="3" constant="true"/>
+</listOfCompartments>
+
+<layout:listOfLayouts xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+<layout:layout layout:id="Layout_1">
+<layout:dimensions layout:width="400" layout:height="230"/>
+<layout:listOfCompartmentGlyphs>
+<layout:compartmentGlyph layout:id="CompartmentGlyph_1" layout:compartment="Yeast">
+<layout:boundingBox layout:id="bb1">
+<layout:position layout:x="5" layout:y="5"/>
+<layout:dimensions layout:width="390" layout:height="220"/>
+</layout:boundingBox>
+</layout:compartmentGlyph>
+</layout:listOfCompartmentGlyphs>
+
+</layout:layout>
+</layout:listOfLayouts>
+</model>
+</sbml>
\ No newline at end of file
diff --git a/converter-sbml/testFiles/layoutExample/Complete_Example.xml b/converter-sbml/testFiles/layoutExample/Complete_Example.xml
new file mode 100644
index 0000000000000000000000000000000000000000..d7081bf344afa5318c871d6c91fcc7e3a1e6e6ac
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/Complete_Example.xml
@@ -0,0 +1,262 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"
+xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1"
+level="3" version="1" layout:required="false" >
+<model id="TestModel_with_modifiers" timeUnits="time">
+<listOfUnitDefinitions>
+<unitDefinition id="volume">
+<listOfUnits>
+<unit kind="litre" exponent="1" scale="0" multiplier="1"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition id="substance">
+<listOfUnits>
+<unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition id="time">
+<listOfUnits>
+<unit kind="second" exponent="1" scale="0" multiplier="1"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment id="Yeast" spatialDimensions="3" units="volume" constant="true"/>
+</listOfCompartments>
+<listOfSpecies>
+<species id="Glucose" compartment="Yeast" substanceUnits="substance"
+hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+<species id="G6P" name="Glucose-6-phosphate" compartment="Yeast"
+substanceUnits="substance" hasOnlySubstanceUnits="false"
+boundaryCondition="false" constant="false"/>
+<species id="ATP" compartment="Yeast" substanceUnits="substance"
+hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+<species id="ADP" compartment="Yeast" substanceUnits="substance"
+hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+<species id="Pi" compartment="Yeast" substanceUnits="substance"
+hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+</listOfSpecies>
+<listOfReactions>
+<reaction id="Hexokinase" reversible="false" fast="false">
+<listOfReactants>
+<speciesReference id="SpeciesReference_Glucose" species="Glucose"
+stoichiometry="1" constant="true"/>
+<speciesReference id="SpeciesReference_ATP" species="ATP"
+stoichiometry="1" constant="true"/>
+</listOfReactants>
+<listOfProducts>
+<speciesReference id="SpeciesReference_G6P" species="G6P"
+stoichiometry="1" constant="true"/>
+<speciesReference id="SpeciesReference_ADP" species="ADP"
+stoichiometry="1" constant="true"/>
+</listOfProducts>
+<listOfModifiers>
+<modifierSpeciesReference id="ModifierSpeciesReference_G6P" species="G6P"/>
+<modifierSpeciesReference id="ModifierSpeciesReference_Pi" species="Pi"/>
+</listOfModifiers>
+</reaction>
+</listOfReactions>
+<layout:listOfLayouts xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+<layout:layout layout:id="Layout_1">
+<layout:dimensions layout:width="400" layout:height="230"/>
+<layout:listOfCompartmentGlyphs>
+<layout:compartmentGlyph layout:id="CompartmentGlyph_1" layout:compartment="Yeast">
+<layout:boundingBox layout:id="bb1">
+<layout:position layout:x="5" layout:y="5"/>
+<layout:dimensions layout:width="390" layout:height="220"/>
+</layout:boundingBox>
+</layout:compartmentGlyph>
+</layout:listOfCompartmentGlyphs>
+<layout:listOfSpeciesGlyphs>
+<layout:speciesGlyph layout:id="SpeciesGlyph_Glucose" layout:species="Glucose">
+<layout:boundingBox layout:id="bb2">
+<layout:position layout:x="105" layout:y="20"/>
+<layout:dimensions layout:width="130" layout:height="20"/>
+</layout:boundingBox>
+</layout:speciesGlyph>
+<layout:speciesGlyph layout:id="SpeciesGlyph_G6P" layout:species="G6P">
+<layout:boundingBox layout:id="bb5">
+<layout:position layout:x="50" layout:y="190"/>
+<layout:dimensions layout:width="270" layout:height="20"/>
+</layout:boundingBox>
+</layout:speciesGlyph>
+<layout:speciesGlyph layout:id="SpeciesGlyph_ATP" layout:species="ATP">
+<layout:boundingBox layout:id="bb3">
+<layout:position layout:x="270" layout:y="70"/>
+<layout:dimensions layout:width="80" layout:height="20"/>
+</layout:boundingBox>
+</layout:speciesGlyph>
+<layout:speciesGlyph layout:id="glyph_ADP" layout:species="ADP">
+<layout:boundingBox layout:id="bb4">
+<layout:position layout:x="270" layout:y="140"/>
+<layout:dimensions layout:width="80" layout:height="20"/>
+</layout:boundingBox>
+</layout:speciesGlyph>
+<layout:speciesGlyph layout:id="SpeciesGlyph_Pi" layout:species="Pi">
+<layout:boundingBox layout:id="bb6">
+<layout:position layout:x="50" layout:y="100"/>
+<layout:dimensions layout:width="60" layout:height="20"/>
+</layout:boundingBox>
+</layout:speciesGlyph>
+</layout:listOfSpeciesGlyphs>
+<layout:listOfReactionGlyphs>
+<layout:reactionGlyph layout:id="glyph_Hexokinase" layout:reaction="Hexokinase">
+<layout:curve>
+<layout:listOfCurveSegments>
+<layout:curveSegment
+xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+xsi:type="LineSegment">
+<layout:start layout:x="170" layout:y="100"/>
+<layout:end layout:x="170" layout:y="130"/>
+</layout:curveSegment>
+</layout:listOfCurveSegments>
+</layout:curve>
+<layout:listOfSpeciesReferenceGlyphs>
+<layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_Glucose"
+layout:speciesReference="SpeciesReference_Glucose"
+layout:speciesGlyph="SpeciesGlyph_Glucose"
+layout:role="substrate">
+<layout:curve>
+<layout:listOfCurveSegments>
+<layout:curveSegment
+xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+xsi:type="LineSegment">
+<layout:start layout:x="170" layout:y="100"/>
+<layout:end layout:x="170" layout:y="50"/>
+</layout:curveSegment>
+</layout:listOfCurveSegments>
+</layout:curve>
+</layout:speciesReferenceGlyph>
+<layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_ATP"
+layout:speciesReference="SpeciesReference_ATP"
+layout:speciesGlyph="SpeciesGlyph_ATP"
+layout:role="sidesubstrate">
+<layout:curve>
+<layout:listOfCurveSegments>
+<layout:curveSegment
+xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+xsi:type="CubicBezier">
+<layout:start layout:x="170" layout:y="100"/>
+<layout:end layout:x="260" layout:y="80"/>
+<layout:basePoint1 layout:x="170" layout:y="80"/>
+<layout:basePoint2 layout:x="170" layout:y="80"/>
+</layout:curveSegment>
+</layout:listOfCurveSegments>
+</layout:curve>
+</layout:speciesReferenceGlyph>
+<layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_G6P_1"
+layout:speciesReference="SpeciesReference_G6P"
+layout:speciesGlyph="SpeciesGlyph_G6P"
+layout:role="product">
+<layout:curve>
+<layout:listOfCurveSegments>
+<layout:curveSegment
+xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+xsi:type="LineSegment">
+<layout:start layout:x="170" layout:y="130"/>
+<layout:end layout:x="170" layout:y="180"/>
+</layout:curveSegment>
+</layout:listOfCurveSegments>
+</layout:curve>
+</layout:speciesReferenceGlyph>
+<layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_ADP"
+layout:speciesReference="SpeciesReference_ADP"
+layout:speciesGlyph="glyph_ADP"
+layout:role="sideproduct">
+<layout:curve>
+<layout:listOfCurveSegments>
+<layout:curveSegment
+xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+xsi:type="CubicBezier">
+<layout:start layout:x="170" layout:y="130"/>
+<layout:end layout:x="260" layout:y="150"/>
+<layout:basePoint1 layout:x="170" layout:y="150"/>
+<layout:basePoint2 layout:x="170" layout:y="150"/>
+</layout:curveSegment>
+</layout:listOfCurveSegments>
+</layout:curve>
+</layout:speciesReferenceGlyph>
+<layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_G6P_2"
+layout:speciesReference="ModifierSpeciesReference_G6P"
+layout:speciesGlyph="SpeciesGlyph_G6P"
+layout:role="inhibitor">
+<layout:curve>
+<layout:listOfCurveSegments>
+<layout:curveSegment
+xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+xsi:type="CubicBezier">
+<layout:start layout:x="45" layout:y="200"/>
+<layout:end layout:x="165" layout:y="120"/>
+<layout:basePoint1 layout:x="0" layout:y="200"/>
+<layout:basePoint2 layout:x="0" layout:y="120"/>
+</layout:curveSegment>
+</layout:listOfCurveSegments>
+</layout:curve>
+</layout:speciesReferenceGlyph>
+<layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_PI"
+layout:speciesReference="ModifierSpeciesReference_Pi"
+layout:speciesGlyph="SpeciesGlyph_Pi"
+layout:role="activator">
+<layout:curve>
+<layout:listOfCurveSegments>
+<layout:curveSegment
+xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+xsi:type="CubicBezier">
+<layout:start layout:x="115" layout:y="110"/>
+<layout:end layout:x="165" layout:y="110"/>
+<layout:basePoint1 layout:x="140" layout:y="110"/>
+<layout:basePoint2 layout:x="140" layout:y="110"/>
+</layout:curveSegment>
+</layout:listOfCurveSegments>
+</layout:curve>
+</layout:speciesReferenceGlyph>
+</layout:listOfSpeciesReferenceGlyphs>
+</layout:reactionGlyph>
+</layout:listOfReactionGlyphs>
+<layout:listOfTextGlyphs>
+<layout:textGlyph layout:id="TextGlyph_Glucose"
+layout:originOfText="Glucose"
+layout:graphicalObject="SpeciesGlyph_Glucose">
+<layout:boundingBox layout:id="bbA">
+<layout:position layout:x="115" layout:y="20"/>
+<layout:dimensions layout:width="110" layout:height="20"/>
+</layout:boundingBox>
+</layout:textGlyph>
+<layout:textGlyph layout:id="TextGlyph_G6P"
+layout:originOfText="G6P"
+layout:graphicalObject="SpeciesGlyph_G6P">
+<layout:boundingBox layout:id="bbD">
+<layout:position layout:x="60" layout:y="190"/>
+<layout:dimensions layout:width="250" layout:height="20"/>
+</layout:boundingBox>
+</layout:textGlyph>
+<layout:textGlyph layout:id="TextGlyph_ATP"
+layout:originOfText="ATP"
+layout:graphicalObject="SpeciesGlyph_ATP">
+<layout:boundingBox layout:id="bbB">
+<layout:position layout:x="280" layout:y="70"/>
+<layout:dimensions layout:width="60" layout:height="20"/>
+</layout:boundingBox>
+</layout:textGlyph>
+<layout:textGlyph layout:id="TextGlyph_ADP"
+layout:originOfText="ADP"
+layout:graphicalObject="glyph_ADP">
+<layout:boundingBox layout:id="bbC">
+<layout:position layout:x="280" layout:y="140"/>
+<layout:dimensions layout:width="60" layout:height="20"/>
+</layout:boundingBox>
+</layout:textGlyph>
+<layout:textGlyph layout:id="TextGlyph_PI"
+layout:originOfText="Pi"
+layout:graphicalObject="SpeciesGlyph_Pi">
+<layout:boundingBox layout:id="bbE">
+<layout:position layout:x="60" layout:y="100"/>
+<layout:dimensions layout:width="40" layout:height="20"/>
+</layout:boundingBox>
+</layout:textGlyph>
+</layout:listOfTextGlyphs>
+</layout:layout>
+</layout:listOfLayouts>
+</model>
+</sbml>
\ No newline at end of file
diff --git a/converter-sbml/testFiles/layoutExample/Complete_Example_level2.xml b/converter-sbml/testFiles/layoutExample/Complete_Example_level2.xml
new file mode 100644
index 0000000000000000000000000000000000000000..ce678f269f3e51da8491354671dad45efe83531c
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/Complete_Example_level2.xml
@@ -0,0 +1,240 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+<model id="TestModel_with_modifiers">
+<annotation>
+<listOfLayouts xmlns="http://projects.eml.org/bcb/sbml/level2"
+xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+<layout id="Layout_1">
+<dimensions width="400" height="230"/>
+<listOfCompartmentGlyphs>
+<compartmentGlyph id="CompartmentGlyph_1" compartment="Yeast">
+<boundingBox id="bb1">
+<position x="5" y="5"/>
+<dimensions width="390" height="220"/>
+</boundingBox>
+</compartmentGlyph>
+</listOfCompartmentGlyphs>
+<listOfSpeciesGlyphs>
+<speciesGlyph id="SpeciesGlyph_Glucose" species="Glucose">
+<boundingBox id="bb2">
+<position x="105" y="20"/>
+<dimensions width="130" height="20"/>
+</boundingBox>
+</speciesGlyph>
+<speciesGlyph id="SpeciesGlyph_G6P" species="G6P">
+<boundingBox id="bb5">
+<position x="50" y="190"/>
+<dimensions width="270" height="20"/>
+</boundingBox>
+</speciesGlyph>
+<speciesGlyph id="SpeciesGlyph_ATP" species="ATP">
+<boundingBox id="bb3">
+<position x="270" y="70"/>
+<dimensions width="80" height="20"/>
+</boundingBox>
+</speciesGlyph>
+<speciesGlyph id="glyph_ADP" species="ADP">
+<boundingBox id="bb4">
+<position x="270" y="140"/>
+<dimensions width="80" height="20"/>
+</boundingBox>
+</speciesGlyph>
+<speciesGlyph id="SpeciesGlyph_Pi" species="Pi">
+<boundingBox id="bb6">
+<position x="50" y="100"/>
+<dimensions width="60" height="20"/>
+</boundingBox>
+</speciesGlyph>
+</listOfSpeciesGlyphs>
+<listOfReactionGlyphs>
+<reactionGlyph id="glyph_Hexokinase" reaction="Hexokinase">
+<curve>
+<listOfCurveSegments>
+<curveSegment xsi:type="LineSegment">
+<start x="170" y="100"/>
+<end x="170" y="130"/>
+</curveSegment>
+</listOfCurveSegments>
+</curve>
+<listOfSpeciesReferenceGlyphs>
+<speciesReferenceGlyph id="SpeciesReferenceGlyph_Glucose"
+speciesReference="SpeciesReference_Glucose"
+speciesGlyph="SpeciesGlyph_Glucose" role="substrate">
+<curve>
+<listOfCurveSegments>
+<curveSegment xsi:type="LineSegment">
+<start x="170" y="100"/>
+<end x="170" y="50"/>
+</curveSegment>
+</listOfCurveSegments>
+</curve>
+</speciesReferenceGlyph>
+<speciesReferenceGlyph id="SpeciesReferenceGlyph_ATP"
+speciesReference="SpeciesReference_ATP"
+speciesGlyph="SpeciesGlyph_ATP" role="sidesubstrate">
+<curve>
+<listOfCurveSegments>
+<curveSegment xsi:type="CubicBezier">
+<start x="170" y="100"/>
+<end x="260" y="80"/>
+<basePoint1 x="170" y="80"/>
+<basePoint2 x="170" y="80"/>
+</curveSegment>
+</listOfCurveSegments>
+</curve>
+</speciesReferenceGlyph>
+<speciesReferenceGlyph id="SpeciesReferenceGlyph_G6P_1"
+speciesReference="SpeciesReference_G6P"
+speciesGlyph="SpeciesGlyph_G6P" role="product">
+<curve>
+<listOfCurveSegments>
+<curveSegment xsi:type="LineSegment">
+<start x="170" y="130"/>
+<end x="170" y="180"/>
+</curveSegment>
+</listOfCurveSegments>
+</curve>
+</speciesReferenceGlyph>
+<speciesReferenceGlyph id="SpeciesReferenceGlyph_ADP"
+speciesReference="SpeciesReference_ADP"
+speciesGlyph="glyph_ADP" role="sideproduct">
+<curve>
+<listOfCurveSegments>
+<curveSegment xsi:type="CubicBezier">
+<start x="170" y="130"/>
+<end x="260" y="150"/>
+<basePoint1 x="170" y="150"/>
+<basePoint2 x="170" y="150"/>
+</curveSegment>
+</listOfCurveSegments>
+</curve>
+</speciesReferenceGlyph>
+<speciesReferenceGlyph id="SpeciesReferenceGlyph_G6P_2"
+speciesReference="ModifierSpeciesReference_G6P"
+speciesGlyph="SpeciesGlyph_G6P" role="inhibitor">
+<curve>
+<listOfCurveSegments>
+<curveSegment xsi:type="CubicBezier">
+<start x="45" y="200"/>
+<end x="165" y="120"/>
+<basePoint1 x="0" y="200"/>
+<basePoint2 x="0" y="120"/>
+</curveSegment>
+</listOfCurveSegments>
+</curve>
+</speciesReferenceGlyph>
+<speciesReferenceGlyph id="SpeciesReferenceGlyph_PI"
+speciesReference="ModifierSpeciesReference_Pi"
+speciesGlyph="SpeciesGlyph_Pi" role="activator">
+<curve>
+<listOfCurveSegments>
+<curveSegment xsi:type="CubicBezier">
+<start x="115" y="110"/>
+<end x="165" y="110"/>
+<basePoint1 x="140" y="110"/>
+<basePoint2 x="140" y="110"/>
+</curveSegment>
+</listOfCurveSegments>
+</curve>
+</speciesReferenceGlyph>
+</listOfSpeciesReferenceGlyphs>
+</reactionGlyph>
+</listOfReactionGlyphs>
+<listOfTextGlyphs>
+<textGlyph id="TextGlyph_Glucose" graphicalObject="SpeciesGlyph_Glucose"
+originOfText="Glucose">
+<boundingBox id="bbA">
+<position x="115" y="20"/>
+<dimensions width="110" height="20"/>
+</boundingBox>
+</textGlyph>
+<textGlyph id="TextGlyph_G6P" graphicalObject="SpeciesGlyph_G6P"
+originOfText="G6P">
+<boundingBox id="bbD">
+<position x="60" y="190"/>
+<dimensions width="250" height="20"/>
+</boundingBox>
+</textGlyph>
+<textGlyph id="TextGlyph_ATP" graphicalObject="SpeciesGlyph_ATP"
+originOfText="ATP">
+<boundingBox id="bbB">
+<position x="280" y="70"/>
+<dimensions width="60" height="20"/>
+</boundingBox>
+</textGlyph>
+<textGlyph id="TextGlyph_ADP" graphicalObject="glyph_ADP"
+originOfText="ADP">
+<boundingBox id="bbC">
+<position x="280" y="140"/>
+<dimensions width="60" height="20"/>
+</boundingBox>
+</textGlyph>
+<textGlyph id="TextGlyph_PI" graphicalObject="SpeciesGlyph_Pi"
+originOfText="Pi">
+<boundingBox id="bbE">
+<position x="60" y="100"/>
+<dimensions width="40" height="20"/>
+</boundingBox>
+</textGlyph>
+</listOfTextGlyphs>
+</layout>
+</listOfLayouts>
+</annotation>
+<listOfCompartments>
+<compartment id="Yeast"/>
+</listOfCompartments>
+<listOfSpecies>
+<species id="Glucose" compartment="Yeast"/>
+<species id="G6P" name="Glucose-6-phosphate" compartment="Yeast"/>
+<species id="ATP" compartment="Yeast"/>
+<species id="ADP" compartment="Yeast"/>
+<species id="Pi" compartment="Yeast"/>
+</listOfSpecies>
+<listOfReactions>
+<reaction id="Hexokinase" reversible="false">
+<listOfReactants>
+<speciesReference species="Glucose">
+<annotation>
+<layoutId xmlns="http://projects.eml.org/bcb/sbml/level2"
+id="SpeciesReference_Glucose"/>
+</annotation>
+</speciesReference>
+<speciesReference species="ATP">
+<annotation>
+<layoutId xmlns="http://projects.eml.org/bcb/sbml/level2"
+id="SpeciesReference_ATP"/>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference species="G6P">
+<annotation>
+<layoutId xmlns="http://projects.eml.org/bcb/sbml/level2"
+id="SpeciesReference_G6P"/>
+</annotation>
+</speciesReference>
+<speciesReference species="ADP">
+<annotation>
+<layoutId xmlns="http://projects.eml.org/bcb/sbml/level2"
+id="SpeciesReference_ADP"/>
+</annotation>
+</speciesReference>
+</listOfProducts>
+<listOfModifiers>
+<modifierSpeciesReference species="G6P">
+<annotation>
+<layoutId xmlns="http://projects.eml.org/bcb/sbml/level2"
+id="ModifierSpeciesReference_G6P"/>
+</annotation>
+</modifierSpeciesReference>
+<modifierSpeciesReference species="Pi">
+<annotation>
+<layoutId xmlns="http://projects.eml.org/bcb/sbml/level2"
+id="ModifierSpeciesReference_Pi"/>
+</annotation>
+</modifierSpeciesReference>
+</listOfModifiers>
+</reaction>
+</listOfReactions>
+</model>
+</sbml>
\ No newline at end of file
diff --git a/converter-sbml/testFiles/layoutExample/Complete_Example_level2_level3.xml b/converter-sbml/testFiles/layoutExample/Complete_Example_level2_level3.xml
new file mode 100644
index 0000000000000000000000000000000000000000..cf69dabb37c87d47b796772e0292f33ca3603e0f
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/Complete_Example_level2_level3.xml
@@ -0,0 +1,209 @@
+<?xml version='1.0' encoding='utf-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" layout:required="false" level="3" version="1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+ <model areaUnits="area" extentUnits="substance" id="TestModel_with_modifiers" lengthUnits="metre" substanceUnits="substance" timeUnits="second" volumeUnits="volume">
+ <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <layout:layout layout:id="Layout_1">
+ <layout:dimensions layout:height="230" layout:width="400" />
+ <layout:listOfCompartmentGlyphs>
+ <layout:compartmentGlyph layout:compartment="Yeast" layout:id="CompartmentGlyph_1">
+ <layout:boundingBox layout:id="bb1">
+ <layout:position layout:x="5" layout:y="5" />
+ <layout:dimensions layout:height="220" layout:width="390" />
+ </layout:boundingBox>
+ </layout:compartmentGlyph>
+ </layout:listOfCompartmentGlyphs>
+ <layout:listOfSpeciesGlyphs>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_Glucose" layout:species="Glucose">
+ <layout:boundingBox layout:id="bb2">
+ <layout:position layout:x="105" layout:y="20" />
+ <layout:dimensions layout:height="20" layout:width="130" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_G6P" layout:species="G6P">
+ <layout:boundingBox layout:id="bb5">
+ <layout:position layout:x="50" layout:y="190" />
+ <layout:dimensions layout:height="20" layout:width="270" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_ATP" layout:species="ATP">
+ <layout:boundingBox layout:id="bb3">
+ <layout:position layout:x="270" layout:y="70" />
+ <layout:dimensions layout:height="20" layout:width="80" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="glyph_ADP" layout:species="ADP">
+ <layout:boundingBox layout:id="bb4">
+ <layout:position layout:x="270" layout:y="140" />
+ <layout:dimensions layout:height="20" layout:width="80" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_Pi" layout:species="Pi">
+ <layout:boundingBox layout:id="bb6">
+ <layout:position layout:x="50" layout:y="100" />
+ <layout:dimensions layout:height="20" layout:width="60" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ </layout:listOfSpeciesGlyphs>
+ <layout:listOfReactionGlyphs>
+ <layout:reactionGlyph layout:id="glyph_Hexokinase" layout:reaction="Hexokinase">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="LineSegment">
+ <layout:start layout:x="170" layout:y="100" />
+ <layout:end layout:x="170" layout:y="130" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ <layout:listOfSpeciesReferenceGlyphs>
+ <layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_Glucose" layout:role="substrate" layout:speciesGlyph="SpeciesGlyph_Glucose"
+ layout:speciesReference="SpeciesReference_Glucose">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="LineSegment">
+ <layout:start layout:x="170" layout:y="100" />
+ <layout:end layout:x="170" layout:y="50" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_ATP" layout:role="sidesubstrate" layout:speciesGlyph="SpeciesGlyph_ATP" layout:speciesReference="SpeciesReference_ATP">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="CubicBezier">
+ <layout:start layout:x="170" layout:y="100" />
+ <layout:end layout:x="260" layout:y="80" />
+ <layout:basePoint1 layout:x="170" layout:y="80" />
+ <layout:basePoint2 layout:x="170" layout:y="80" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_G6P_1" layout:role="product" layout:speciesGlyph="SpeciesGlyph_G6P" layout:speciesReference="SpeciesReference_G6P">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="LineSegment">
+ <layout:start layout:x="170" layout:y="130" />
+ <layout:end layout:x="170" layout:y="180" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_ADP" layout:role="sideproduct" layout:speciesGlyph="glyph_ADP" layout:speciesReference="SpeciesReference_ADP">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="CubicBezier">
+ <layout:start layout:x="170" layout:y="130" />
+ <layout:end layout:x="260" layout:y="150" />
+ <layout:basePoint1 layout:x="170" layout:y="150" />
+ <layout:basePoint2 layout:x="170" layout:y="150" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_G6P_2" layout:role="inhibitor" layout:speciesGlyph="SpeciesGlyph_G6P"
+ layout:speciesReference="ModifierSpeciesReference_G6P">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="CubicBezier">
+ <layout:start layout:x="45" layout:y="200" />
+ <layout:end layout:x="165" layout:y="120" />
+ <layout:basePoint1 layout:x="0" layout:y="200" />
+ <layout:basePoint2 layout:x="0" layout:y="120" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_PI" layout:role="activator" layout:speciesGlyph="SpeciesGlyph_Pi" layout:speciesReference="ModifierSpeciesReference_Pi">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="CubicBezier">
+ <layout:start layout:x="115" layout:y="110" />
+ <layout:end layout:x="165" layout:y="110" />
+ <layout:basePoint1 layout:x="140" layout:y="110" />
+ <layout:basePoint2 layout:x="140" layout:y="110" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ </layout:listOfSpeciesReferenceGlyphs>
+ </layout:reactionGlyph>
+ </layout:listOfReactionGlyphs>
+ <layout:listOfTextGlyphs>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_Glucose" layout:id="TextGlyph_Glucose" layout:originOfText="Glucose">
+ <layout:boundingBox layout:id="bbA">
+ <layout:position layout:x="115" layout:y="20" />
+ <layout:dimensions layout:height="20" layout:width="110" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_G6P" layout:id="TextGlyph_G6P" layout:originOfText="G6P">
+ <layout:boundingBox layout:id="bbD">
+ <layout:position layout:x="60" layout:y="190" />
+ <layout:dimensions layout:height="20" layout:width="250" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_ATP" layout:id="TextGlyph_ATP" layout:originOfText="ATP">
+ <layout:boundingBox layout:id="bbB">
+ <layout:position layout:x="280" layout:y="70" />
+ <layout:dimensions layout:height="20" layout:width="60" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_ADP" layout:id="TextGlyph_ADP" layout:originOfText="ADP">
+ <layout:boundingBox layout:id="bbC">
+ <layout:position layout:x="280" layout:y="140" />
+ <layout:dimensions layout:height="20" layout:width="60" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_Pi" layout:id="TextGlyph_PI" layout:originOfText="Pi">
+ <layout:boundingBox layout:id="bbE">
+ <layout:position layout:x="60" layout:y="100" />
+ <layout:dimensions layout:height="20" layout:width="40" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ </layout:listOfTextGlyphs>
+ </layout:layout>
+ </layout:listOfLayouts>
+ <listOfUnitDefinitions>
+ <unitDefinition id="volume">
+ <listOfUnits>
+ <unit exponent="1" kind="litre" multiplier="1" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="substance">
+ <listOfUnits>
+ <unit exponent="1" kind="mole" multiplier="1" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="area">
+ <listOfUnits>
+ <unit exponent="2" kind="metre" multiplier="1" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment constant="true" id="Yeast" spatialDimensions="3" units="volume" />
+ </listOfCompartments>
+ <listOfSpecies>
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="Glucose" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="G6P" name="Glucose-6-phosphate" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="ATP" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="ADP" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="Pi" substanceUnits="substance" />
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction fast="false" id="Hexokinase" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="SpeciesReference_Glucose" species="Glucose" stoichiometry="1" />
+ <speciesReference constant="true" id="SpeciesReference_ATP" species="ATP" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="SpeciesReference_G6P" species="G6P" stoichiometry="1" />
+ <speciesReference constant="true" id="SpeciesReference_ADP" species="ADP" stoichiometry="1" />
+ </listOfProducts>
+ <listOfModifiers>
+ <modifierSpeciesReference id="ModifierSpeciesReference_G6P" species="G6P" />
+ <modifierSpeciesReference id="ModifierSpeciesReference_Pi" species="Pi" />
+ </listOfModifiers>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/converter-sbml/testFiles/layoutExample/GeneralGlyph_Example.xml b/converter-sbml/testFiles/layoutExample/GeneralGlyph_Example.xml
new file mode 100644
index 0000000000000000000000000000000000000000..36861009456fca821f6582c53d9215aa7f95a26b
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/GeneralGlyph_Example.xml
@@ -0,0 +1,84 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"
+xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1"
+level="3" version="1" layout:required="false" >
+<model id="GeneralGlyphExample" >
+<listOfCompartments>
+<compartment id="compartment"
+spatialDimensions="3" size="1" constant="true"/>
+</listOfCompartments>
+<listOfSpecies>
+<species sboTerm="SBO:0000395" id="Node0"
+compartment="compartment" initialConcentration="0"
+hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+<species sboTerm="SBO:0000395" id="Node1"
+compartment="compartment" initialConcentration="0"
+hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+</listOfSpecies>
+<layout:listOfLayouts
+xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+<layout:layout layout:id="example">
+<layout:dimensions layout:width="239.037328720093" layout:height="76.5"/>
+<layout:listOfSpeciesGlyphs>
+<layout:speciesGlyph layout:id="sGlyph_0" layout:species="Node0" >
+<layout:boundingBox>
+<layout:position layout:x="16" layout:y="18"/>
+<layout:dimensions layout:width="62" layout:height="40"/>
+</layout:boundingBox>
+</layout:speciesGlyph>
+<layout:speciesGlyph layout:id="sGlyph_1" layout:species="Node1" >
+<layout:boundingBox>
+<layout:position layout:x="161" layout:y="18"/>
+<layout:dimensions layout:width="62" layout:height="40"/>
+</layout:boundingBox>
+</layout:speciesGlyph>
+</layout:listOfSpeciesGlyphs>
+<layout:listOfAdditionalGraphicalObjects>
+<layout:generalGlyph layout:id="rGlyph_0" layout:reference="sGlyph_0">
+<!-- unused bounding box -->
+<layout:boundingBox>
+<layout:position layout:x="0" layout:y="0"/>
+<layout:dimensions layout:width="0" layout:height="0"/>
+</layout:boundingBox>
+<layout:listOfReferenceGlyphs>
+<!-- reference glyph representing the inhibited species -->
+<layout:referenceGlyph
+layout:id="SpeciesReference_J0_0"
+layout:reference="Node1"
+layout:glyph="sGlyph_1"
+layout:role="inhibitor">
+<layout:curve>
+<layout:listOfCurveSegments>
+<layout:curveSegment
+xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+xsi:type="LineSegment">
+<layout:start layout:x="86" layout:y="38"/>
+<layout:end layout:x="153" layout:y="38"/>
+</layout:curveSegment>
+</layout:listOfCurveSegments>
+</layout:curve>
+</layout:referenceGlyph>
+</layout:listOfReferenceGlyphs>
+</layout:generalGlyph>
+</layout:listOfAdditionalGraphicalObjects>
+<layout:listOfTextGlyphs>
+<layout:textGlyph layout:id="tGlyph_0" layout:text="Node0"
+layout:graphicalObject="sGlyph_0">
+<layout:boundingBox>
+<layout:position layout:x="16" layout:y="18"/>
+<layout:dimensions layout:width="62" layout:height="40"/>
+</layout:boundingBox>
+</layout:textGlyph>
+<layout:textGlyph layout:id="tGlyph_1" layout:text="Node1"
+layout:graphicalObject="sGlyph_1">
+<layout:boundingBox>
+<layout:position layout:x="161" layout:y="18"/>
+<layout:dimensions layout:width="62" layout:height="40"/>
+</layout:boundingBox>
+</layout:textGlyph>
+</layout:listOfTextGlyphs>
+</layout:layout>
+</layout:listOfLayouts>
+</model>
+</sbml>
\ No newline at end of file
diff --git a/converter-sbml/testFiles/layoutExample/README.MD b/converter-sbml/testFiles/layoutExample/README.MD
new file mode 100644
index 0000000000000000000000000000000000000000..3466991539326359d2de6557b6622f283021a30e
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/README.MD
@@ -0,0 +1 @@
+example files taken from: https://github.com/NRNB-GSoC2017-SBML2SBGNML-Converters/SBML2SBGNML
\ No newline at end of file
diff --git a/converter-sbml/testFiles/layoutExample/ReactionGlyph_Example.xml b/converter-sbml/testFiles/layoutExample/ReactionGlyph_Example.xml
new file mode 100644
index 0000000000000000000000000000000000000000..189da3871f8be71bd50ceec690db47fe7725ccb2
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/ReactionGlyph_Example.xml
@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"
+xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1"
+level="3" version="1" layout:required="false" >
+<model id="TestModel_with_modifiers">
+<listOfReactions>
+<reaction id="Hexokinase" reversible="false" fast="false">
+</reaction>
+</listOfReactions>
+<layout:listOfLayouts xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+<layout:layout layout:id="Layout_1">
+<layout:dimensions layout:width="400" layout:height="230"/>
+<layout:listOfReactionGlyphs>
+<layout:reactionGlyph layout:id="glyph_Hexokinase" layout:reaction="Hexokinase">
+<layout:curve>
+<layout:listOfCurveSegments>
+<layout:curveSegment
+xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+xsi:type="LineSegment">
+<layout:start layout:x="170" layout:y="100"/>
+<layout:end layout:x="170" layout:y="130"/>
+</layout:curveSegment>
+</layout:listOfCurveSegments>
+</layout:curve>
+<layout:listOfSpeciesReferenceGlyphs>
+</layout:listOfSpeciesReferenceGlyphs>
+</layout:reactionGlyph>
+</layout:listOfReactionGlyphs>
+</layout:layout>
+</layout:listOfLayouts>
+</model>
+</sbml>
\ No newline at end of file
diff --git a/converter-sbml/testFiles/layoutExample/ReactionGlyph_Example_level2+id.xml b/converter-sbml/testFiles/layoutExample/ReactionGlyph_Example_level2+id.xml
new file mode 100644
index 0000000000000000000000000000000000000000..17dbcc923ef5089c7da9b364f0fa344f41492030
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/ReactionGlyph_Example_level2+id.xml
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+<model id="TestModel_with_modifiers">
+<annotation>
+<listOfLayouts xmlns="http://projects.eml.org/bcb/sbml/level2"
+xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+<layout id="Layout_1">
+<dimensions width="400" height="230">
+</dimensions>
+<listOfReactionGlyphs>
+<reactionGlyph id="glyph_Hexokinase" reaction="Hexokinase">
+<listOfSpeciesReferenceGlyphs>
+<speciesReferenceGlyph id="SpeciesReferenceGlyph_Glucose"
+speciesReference="SpeciesReference_Glucose"
+speciesGlyph="SpeciesGlyph_Glucose" role="substrate">
+<curve>
+<listOfCurveSegments>
+<curveSegment xsi:type="LineSegment">
+<start x="170" y="100">
+</start>
+<end x="170" y="50">
+</end>
+</curveSegment>
+</listOfCurveSegments>
+</curve>
+</speciesReferenceGlyph>
+</listOfSpeciesReferenceGlyphs>
+</reactionGlyph>
+</listOfReactionGlyphs>
+</layout>
+</listOfLayouts>
+</annotation>
+<listOfReactions>
+<reaction id="Hexokinase" reversible="false">
+<listOfReactants>
+<speciesReference species="Glucose">
+<annotation>
+<layoutId xmlns="http://projects.eml.org/bcb/sbml/level2"
+id="SpeciesReference_Glucose"/>
+</annotation>
+</speciesReference>
+</listOfReactants>
+</reaction>
+</listOfReactions>
+</model>
+</sbml>
\ No newline at end of file
diff --git a/converter-sbml/testFiles/layoutExample/ReactionGlyph_Example_level2+id_level3.xml b/converter-sbml/testFiles/layoutExample/ReactionGlyph_Example_level2+id_level3.xml
new file mode 100644
index 0000000000000000000000000000000000000000..b7305073f14fee45351c9359b4d807dab3c9f735
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/ReactionGlyph_Example_level2+id_level3.xml
@@ -0,0 +1,45 @@
+<?xml version='1.0' encoding='utf-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" layout:required="false" level="3" version="1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+ <model areaUnits="area" extentUnits="mole" id="TestModel_with_modifiers" lengthUnits="metre" substanceUnits="mole" timeUnits="second" volumeUnits="litre">
+ <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <layout:layout layout:id="Layout_1">
+ <layout:dimensions layout:height="230" layout:width="400" />
+ <layout:listOfReactionGlyphs>
+ <layout:reactionGlyph layout:id="glyph_Hexokinase" layout:reaction="Hexokinase">
+ <layout:boundingBox>
+ <layout:position layout:x="0" layout:y="0" />
+ <layout:dimensions layout:height="0" layout:width="0" />
+ </layout:boundingBox>
+ <layout:listOfSpeciesReferenceGlyphs>
+ <layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_Glucose" layout:role="substrate" layout:speciesGlyph="SpeciesGlyph_Glucose"
+ layout:speciesReference="SpeciesReference_Glucose">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="LineSegment">
+ <layout:start layout:x="170" layout:y="100" />
+ <layout:end layout:x="170" layout:y="50" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ </layout:listOfSpeciesReferenceGlyphs>
+ </layout:reactionGlyph>
+ </layout:listOfReactionGlyphs>
+ </layout:layout>
+ </layout:listOfLayouts>
+ <listOfUnitDefinitions>
+ <unitDefinition id="area">
+ <listOfUnits>
+ <unit exponent="2" kind="metre" multiplier="1" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfReactions>
+ <reaction fast="false" id="Hexokinase" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="SpeciesReference_Glucose" species="Glucose" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/converter-sbml/testFiles/layoutExample/ReactionGlyph_Example_level2.xml b/converter-sbml/testFiles/layoutExample/ReactionGlyph_Example_level2.xml
new file mode 100644
index 0000000000000000000000000000000000000000..7be5743457fa27a31bb2a499cc20fe63ce384da2
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/ReactionGlyph_Example_level2.xml
@@ -0,0 +1,31 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+<model id="TestModel_with_modifiers">
+<annotation>
+<listOfLayouts xmlns="http://projects.eml.org/bcb/sbml/level2"
+xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+<layout id="Layout_1">
+<dimensions width="400" height="230"/>
+<listOfReactionGlyphs>
+<reactionGlyph id="glyph_Hexokinase" reaction="Hexokinase">
+<curve>
+<listOfCurveSegments>
+<curveSegment xsi:type="LineSegment">
+<start x="170" y="100"/>
+<end x="170" y="130"/>
+</curveSegment>
+</listOfCurveSegments>
+</curve>
+<listOfSpeciesReferenceGlyphs>
+</listOfSpeciesReferenceGlyphs>
+</reactionGlyph>
+</listOfReactionGlyphs>
+</layout>
+</listOfLayouts>
+</annotation>
+<listOfReactions>
+<reaction id="Hexokinase" reversible="false">
+</reaction>
+</listOfReactions>
+</model>
+</sbml>
\ No newline at end of file
diff --git a/converter-sbml/testFiles/layoutExample/ReactionGlyph_Example_level2_level3.xml b/converter-sbml/testFiles/layoutExample/ReactionGlyph_Example_level2_level3.xml
new file mode 100644
index 0000000000000000000000000000000000000000..f24034f3f6141001d47633a015b6ded86989dd30
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/ReactionGlyph_Example_level2_level3.xml
@@ -0,0 +1,32 @@
+<?xml version='1.0' encoding='utf-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" layout:required="false" level="3" version="1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+ <model areaUnits="area" extentUnits="mole" id="TestModel_with_modifiers" lengthUnits="metre" substanceUnits="mole" timeUnits="second" volumeUnits="litre">
+ <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <layout:layout layout:id="Layout_1">
+ <layout:dimensions layout:height="230" layout:width="400" />
+ <layout:listOfReactionGlyphs>
+ <layout:reactionGlyph layout:id="glyph_Hexokinase" layout:reaction="Hexokinase">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="LineSegment">
+ <layout:start layout:x="170" layout:y="100" />
+ <layout:end layout:x="170" layout:y="130" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:reactionGlyph>
+ </layout:listOfReactionGlyphs>
+ </layout:layout>
+ </layout:listOfLayouts>
+ <listOfUnitDefinitions>
+ <unitDefinition id="area">
+ <listOfUnits>
+ <unit exponent="2" kind="metre" multiplier="1" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfReactions>
+ <reaction fast="false" id="Hexokinase" reversible="false" />
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/converter-sbml/testFiles/layoutExample/SBML.xml b/converter-sbml/testFiles/layoutExample/SBML.xml
new file mode 100644
index 0000000000000000000000000000000000000000..44ecb49022a1611dd14a4e90f220f8c742c876af
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/SBML.xml
@@ -0,0 +1,87 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="2" version="3" xmlns="http://www.sbml.org/sbml/level2/version3">
+ <model name="EnzymaticReaction">
+ <listOfUnitDefinitions>
+ <unitDefinition id="per_second">
+ <listOfUnits>
+ <unit kind="second" exponent="-1"/>
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="litre_per_mole_per_second">
+ <listOfUnits>
+ <unit kind="mole" exponent="-1"/>
+ <unit kind="litre" exponent="1"/>
+ <unit kind="second" exponent="-1"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment id="cytosol" size="1e-14"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species compartment="cytosol" id="ES" initialAmount="0" name="ES"/>
+ <species compartment="cytosol" id="P" initialAmount="0" name="P"/>
+ <species compartment="cytosol" id="S" initialAmount="1e-20" name="S"/>
+ <species compartment="cytosol" id="E" initialAmount="5e-21" name="E"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="veq">
+ <listOfReactants>
+ <speciesReference species="E"/>
+ <speciesReference species="S"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="ES"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci>cytosol</ci>
+ <apply>
+ <minus/>
+ <apply>
+ <times/>
+ <ci>kon</ci>
+ <ci>E</ci>
+ <ci>S</ci>
+ </apply>
+ <apply>
+ <times/>
+ <ci>koff</ci>
+ <ci>ES</ci>
+ </apply>
+ </apply>
+ </apply>
+ </math>
+ <listOfParameters>
+ <parameter id="kon" value="1000000" units="litre_per_mole_per_second"/>
+ <parameter id="koff" value="0.2" units="per_second"/>
+ </listOfParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="vcat" reversible="false">
+ <listOfReactants>
+ <speciesReference species="ES"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="E"/>
+ <speciesReference species="P"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci>cytosol</ci>
+ <ci>kcat</ci>
+ <ci>ES</ci>
+ </apply>
+ </math>
+ <listOfParameters>
+ <parameter id="kcat" value="0.1" units="per_second"/>
+ </listOfParameters>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/converter-sbml/testFiles/layoutExample/SpeciesGlyph_Example.xml b/converter-sbml/testFiles/layoutExample/SpeciesGlyph_Example.xml
new file mode 100644
index 0000000000000000000000000000000000000000..3c8bfc9ebf8ab1e6e06da83258a2a30f34114796
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/SpeciesGlyph_Example.xml
@@ -0,0 +1,40 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"
+xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1"
+level="3" version="1" layout:required="false" >
+<model id="TestModel_with_modifiers">
+<listOfUnitDefinitions>
+<unitDefinition id="volume">
+<listOfUnits>
+<unit kind="litre" exponent="1" scale="0" multiplier="1"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition id="substance">
+<listOfUnits>
+<unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment id="Yeast" spatialDimensions="3" units="volume" constant="true"/>
+</listOfCompartments>
+<listOfSpecies>
+<species id="Glucose" compartment="Yeast" substanceUnits="substance"
+hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+</listOfSpecies>
+<layout:listOfLayouts xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+<layout:layout layout:id="Layout_1">
+<layout:dimensions layout:width="400" layout:height="230"/>
+<layout:listOfSpeciesGlyphs>
+<layout:speciesGlyph layout:id="SpeciesGlyph_Glucose" layout:species="Glucose">
+<layout:boundingBox layout:id="bb2">
+<layout:position layout:x="105" layout:y="20"/>
+<layout:dimensions layout:width="130" layout:height="20"/>
+</layout:boundingBox>
+</layout:speciesGlyph>
+</layout:listOfSpeciesGlyphs>
+</layout:layout>
+</layout:listOfLayouts>
+</model>
+</sbml>
\ No newline at end of file
diff --git a/converter-sbml/testFiles/layoutExample/SpeciesGlyph_Example_level2.xml b/converter-sbml/testFiles/layoutExample/SpeciesGlyph_Example_level2.xml
new file mode 100644
index 0000000000000000000000000000000000000000..f650353aeafb7a4f77ea8da28b7c360763481baf
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/SpeciesGlyph_Example_level2.xml
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+<model id="TestModel_with_modifiers">
+<annotation>
+<listOfLayouts xmlns="http://projects.eml.org/bcb/sbml/level2"
+xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+<layout id="Layout_1">
+<dimensions width="400" height="230"/>
+<listOfSpeciesGlyphs>
+<speciesGlyph id="SpeciesGlyph_Glucose" species="Glucose">
+<boundingBox id="bb2">
+<position x="105" y="20"/>
+<dimensions width="130" height="20"/>
+</boundingBox>
+</speciesGlyph>
+</listOfSpeciesGlyphs>
+</layout>
+</listOfLayouts>
+</annotation>
+<listOfSpecies>
+<species id="Glucose" compartment="Yeast"/>
+</listOfSpecies>
+</model>
+</sbml>
\ No newline at end of file
diff --git a/converter-sbml/testFiles/layoutExample/SpeciesGlyph_Example_level2_level3.xml b/converter-sbml/testFiles/layoutExample/SpeciesGlyph_Example_level2_level3.xml
new file mode 100644
index 0000000000000000000000000000000000000000..2e1b0315364bab745907fd7646c39c568c5e2aaf
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/SpeciesGlyph_Example_level2_level3.xml
@@ -0,0 +1,33 @@
+<?xml version='1.0' encoding='utf-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" layout:required="false" level="3" version="1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+ <model areaUnits="area" extentUnits="substance" id="TestModel_with_modifiers" lengthUnits="metre" substanceUnits="substance" timeUnits="second" volumeUnits="litre">
+ <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <layout:layout layout:id="Layout_1">
+ <layout:dimensions layout:height="230" layout:width="400" />
+ <layout:listOfSpeciesGlyphs>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_Glucose" layout:species="Glucose">
+ <layout:boundingBox layout:id="bb2">
+ <layout:position layout:x="105" layout:y="20" />
+ <layout:dimensions layout:height="20" layout:width="130" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ </layout:listOfSpeciesGlyphs>
+ </layout:layout>
+ </layout:listOfLayouts>
+ <listOfUnitDefinitions>
+ <unitDefinition id="substance">
+ <listOfUnits>
+ <unit exponent="1" kind="mole" multiplier="1" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="area">
+ <listOfUnits>
+ <unit exponent="2" kind="metre" multiplier="1" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfSpecies>
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="Glucose" substanceUnits="substance" />
+ </listOfSpecies>
+ </model>
+</sbml>
diff --git a/converter-sbml/testFiles/layoutExample/TextGlyph_Example.xml b/converter-sbml/testFiles/layoutExample/TextGlyph_Example.xml
new file mode 100644
index 0000000000000000000000000000000000000000..c6c1377567d35c9078bdeb3c82e9406518887f9f
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/TextGlyph_Example.xml
@@ -0,0 +1,35 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"
+xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1"
+level="3" version="1" layout:required="false" >
+<model id="TestModel_with_modifiers">
+<listOfSpecies>
+<species id="Glucose" compartment="Yeast" substanceUnits="substance"
+hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+</listOfSpecies>
+<layout:listOfLayouts xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+<layout:layout layout:id="Layout_1">
+<layout:dimensions layout:width="400" layout:height="230"/>
+<layout:listOfSpeciesGlyphs>
+<layout:speciesGlyph layout:id="SpeciesGlyph_Glucose" layout:species="Glucose">
+<layout:boundingBox layout:id="bb2">
+<layout:position layout:x="105" layout:y="20"/>
+<layout:dimensions layout:width="130" layout:height="20"/>
+</layout:boundingBox>
+</layout:speciesGlyph>
+</layout:listOfSpeciesGlyphs>
+<layout:listOfTextGlyphs>
+<layout:textGlyph layout:id="TextGlyph_Glucose"
+layout:originOfText="Glucose"
+layout:graphicalObject="SpeciesGlyph_Glucose">
+<layout:boundingBox layout:id="bbA">
+<layout:position layout:x="115" layout:y="20"/>
+<layout:dimensions layout:width="110" layout:height="20"/>
+</layout:boundingBox>
+</layout:textGlyph>
+</layout:listOfTextGlyphs>
+</layout:layout>
+</layout:listOfLayouts>
+</model>
+</sbml>
\ No newline at end of file
diff --git a/converter-sbml/testFiles/layoutExample/TextGlyph_Example_level2.xml b/converter-sbml/testFiles/layoutExample/TextGlyph_Example_level2.xml
new file mode 100644
index 0000000000000000000000000000000000000000..9b32b69abb32e17f97f9a8d4a567d8e14aa9a0a3
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/TextGlyph_Example_level2.xml
@@ -0,0 +1,35 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+<model id="TestModel_with_modifiers">
+<annotation>
+<listOfLayouts xmlns="http://projects.eml.org/bcb/sbml/level2"
+xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+<layout id="Layout_1">
+<dimensions width="400" height="230"/>
+<listOfSpeciesGlyphs>
+<speciesGlyph id="SpeciesGlyph_Glucose" species="Glucose">
+<boundingBox id="bb2">
+<position x="105" y="20"/>
+<dimensions width="130" height="20"/>
+</boundingBox>
+</speciesGlyph>
+</listOfSpeciesGlyphs>
+<listOfTextGlyphs>
+<textGlyph id="TextGlyph_Glucose" graphicalObject="SpeciesGlyph_Glucose"
+originOfText="Glucose">
+<boundingBox id="bbA">
+<position x="115" y="20">
+</position>
+<dimensions width="110" height="20">
+</dimensions>
+</boundingBox>
+</textGlyph>
+</listOfTextGlyphs>
+</layout>
+</listOfLayouts>
+</annotation>
+<listOfSpecies>
+<species id="Glucose" name="Glucose" compartment="Yeast"/>
+</listOfSpecies>
+</model>
+</sbml>
\ No newline at end of file
diff --git a/converter-sbml/testFiles/layoutExample/TextGlyph_Example_level2_level3.xml b/converter-sbml/testFiles/layoutExample/TextGlyph_Example_level2_level3.xml
new file mode 100644
index 0000000000000000000000000000000000000000..cc6221a39a1bdf3250bae2b504a235616944b103
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/TextGlyph_Example_level2_level3.xml
@@ -0,0 +1,41 @@
+<?xml version='1.0' encoding='utf-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" layout:required="false" level="3" version="1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+ <model areaUnits="area" extentUnits="substance" id="TestModel_with_modifiers" lengthUnits="metre" substanceUnits="substance" timeUnits="second" volumeUnits="litre">
+ <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <layout:layout layout:id="Layout_1">
+ <layout:dimensions layout:height="230" layout:width="400" />
+ <layout:listOfSpeciesGlyphs>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_Glucose" layout:species="Glucose">
+ <layout:boundingBox layout:id="bb2">
+ <layout:position layout:x="105" layout:y="20" />
+ <layout:dimensions layout:height="20" layout:width="130" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ </layout:listOfSpeciesGlyphs>
+ <layout:listOfTextGlyphs>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_Glucose" layout:id="TextGlyph_Glucose" layout:originOfText="Glucose">
+ <layout:boundingBox layout:id="bbA">
+ <layout:position layout:x="115" layout:y="20" />
+ <layout:dimensions layout:height="20" layout:width="110" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ </layout:listOfTextGlyphs>
+ </layout:layout>
+ </layout:listOfLayouts>
+ <listOfUnitDefinitions>
+ <unitDefinition id="substance">
+ <listOfUnits>
+ <unit exponent="1" kind="mole" multiplier="1" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="area">
+ <listOfUnits>
+ <unit exponent="2" kind="metre" multiplier="1" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfSpecies>
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="Glucose" name="Glucose" substanceUnits="substance" />
+ </listOfSpecies>
+ </model>
+</sbml>
diff --git a/converter-sbml/testFiles/layoutExample/example1.xml b/converter-sbml/testFiles/layoutExample/example1.xml
new file mode 100644
index 0000000000000000000000000000000000000000..e4bd5229e323481e79b6f758004002f4611f1756
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/example1.xml
@@ -0,0 +1,163 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+ <model id="TestModel">
+ <annotation>
+ <listOfLayouts xmlns="http://projects.eml.org/bcb/sbml/level2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <layout id="Layout_1">
+ <dimensions width="400" height="220"/>
+ <listOfCompartmentGlyphs>
+ <compartmentGlyph id="CompartmentGlyph_1" compartment="Compartment_1">
+ <boundingBox id="bb1">
+ <position x="5" y="5"/>
+ <dimensions width="390" height="210"/>
+ </boundingBox>
+ </compartmentGlyph>
+ </listOfCompartmentGlyphs>
+ <listOfSpeciesGlyphs>
+ <speciesGlyph id="SpeciesGlyph_1" species="Species_1">
+ <boundingBox id="bb2">
+ <position x="80" y="26"/>
+ <dimensions width="240" height="24"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_2" species="Species_2">
+ <boundingBox id="bb3">
+ <position x="80" y="170"/>
+ <dimensions width="240" height="24"/>
+ </boundingBox>
+ </speciesGlyph>
+ </listOfSpeciesGlyphs>
+ <listOfReactionGlyphs>
+ <reactionGlyph id="ReactionGlyph_1" reaction="Reaction_1">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
+ <start x="165" y="105"/>
+ <end x="165" y="115"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ <listOfSpeciesReferenceGlyphs>
+ <speciesReferenceGlyph id="SpeciesReferenceGlyph_1" speciesReference="SpeciesReference_1" speciesGlyph="SpeciesGlyph_1" role="substrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
+ <start x="165" y="105"/>
+ <end x="195" y="60"/>
+ <basePoint1 x="165" y="90"/>
+ <basePoint2 x="165" y="90"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="SpeciesReferenceGlyph_2" speciesReference="SpeciesReference_2" speciesGlyph="SpeciesGlyph_2" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
+ <start x="165" y="115"/>
+ <end x="195" y="160"/>
+ <basePoint1 x="165" y="130"/>
+ <basePoint2 x="165" y="130"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ </listOfSpeciesReferenceGlyphs>
+ </reactionGlyph>
+ <reactionGlyph id="ReactionGlyph_1" reaction="Reaction_2">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
+ <start x="235" y="105"/>
+ <end x="235" y="115"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ <listOfSpeciesReferenceGlyphs>
+ <speciesReferenceGlyph id="SpeciesReferenceGlyph_3" speciesReference="SpeciesReference_3" speciesGlyph="SpeciesGlyph_2" role="substrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
+ <start x="235" y="115"/>
+ <end x="205" y="160"/>
+ <basePoint1 x="235" y="130"/>
+ <basePoint2 x="235" y="130"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="SpeciesReferenceGlyph_4" speciesReference="SpeciesReference_4" speciesGlyph="SpeciesGlyph_1" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
+ <start x="235" y="105"/>
+ <end x="205" y="60"/>
+ <basePoint1 x="235" y="90"/>
+ <basePoint2 x="235" y="90"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ </listOfSpeciesReferenceGlyphs>
+ </reactionGlyph>
+ </listOfReactionGlyphs>
+ <listOfTextGlyphs>
+ <textGlyph id="TextGlyph_01" graphicalObject="SpeciesGlyph_1" originOfText="SpeciesGlyph_1">
+ <boundingBox id="bbA">
+ <position x="92" y="26"/>
+ <dimensions width="228" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_02" graphicalObject="SpeciesGlyph_2" originOfText="SpeciesGlyph_2">
+ <boundingBox id="bbB">
+ <position x="92" y="170"/>
+ <dimensions width="228" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ </listOfTextGlyphs>
+ </layout>
+ </listOfLayouts>
+ </annotation>
+ <listOfCompartments>
+ <compartment id="Compartment_1" size="1"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="Species_1" compartment="Compartment_1" initialConcentration="0"/>
+ <species id="Species_2" compartment="Compartment_1" initialConcentration="0"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="Reaction_1" reversible="false">
+ <listOfReactants>
+ <speciesReference species="Species_1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="SpeciesReference_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Species_2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="SpeciesReference_2"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="Reaction_2" reversible="false">
+ <listOfReactants>
+ <speciesReference species="Species_2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="SpeciesReference_3"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Species_1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="SpeciesReference_4"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/converter-sbml/testFiles/layoutExample/example1_level3.xml b/converter-sbml/testFiles/layoutExample/example1_level3.xml
new file mode 100644
index 0000000000000000000000000000000000000000..3bfa5e56efa33e3e6803913ff5b85dad57b2f9c3
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/example1_level3.xml
@@ -0,0 +1,162 @@
+<?xml version='1.0' encoding='utf-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" layout:required="false" level="3" version="1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+ <model areaUnits="area" extentUnits="substance" id="TestModel" lengthUnits="metre" substanceUnits="substance" timeUnits="second" volumeUnits="volume">
+ <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <layout:layout layout:id="Layout_1">
+ <layout:dimensions layout:height="220" layout:width="400" />
+ <layout:listOfCompartmentGlyphs>
+ <layout:compartmentGlyph layout:compartment="Compartment_1" layout:id="CompartmentGlyph_1">
+ <layout:boundingBox layout:id="bb1">
+ <layout:position layout:x="5" layout:y="5" />
+ <layout:dimensions layout:height="210" layout:width="390" />
+ </layout:boundingBox>
+ </layout:compartmentGlyph>
+ </layout:listOfCompartmentGlyphs>
+ <layout:listOfSpeciesGlyphs>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_1" layout:species="Species_1">
+ <layout:boundingBox layout:id="bb2">
+ <layout:position layout:x="80" layout:y="26" />
+ <layout:dimensions layout:height="24" layout:width="240" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_2" layout:species="Species_2">
+ <layout:boundingBox layout:id="bb3">
+ <layout:position layout:x="80" layout:y="170" />
+ <layout:dimensions layout:height="24" layout:width="240" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ </layout:listOfSpeciesGlyphs>
+ <layout:listOfReactionGlyphs>
+ <layout:reactionGlyph layout:id="ReactionGlyph_1" layout:reaction="Reaction_1">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="LineSegment">
+ <layout:start layout:x="165" layout:y="105" />
+ <layout:end layout:x="165" layout:y="115" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ <layout:listOfSpeciesReferenceGlyphs>
+ <layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_1" layout:role="substrate" layout:speciesGlyph="SpeciesGlyph_1" layout:speciesReference="SpeciesReference_1">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="CubicBezier">
+ <layout:start layout:x="165" layout:y="105" />
+ <layout:end layout:x="195" layout:y="60" />
+ <layout:basePoint1 layout:x="165" layout:y="90" />
+ <layout:basePoint2 layout:x="165" layout:y="90" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_2" layout:role="product" layout:speciesGlyph="SpeciesGlyph_2" layout:speciesReference="SpeciesReference_2">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="CubicBezier">
+ <layout:start layout:x="165" layout:y="115" />
+ <layout:end layout:x="195" layout:y="160" />
+ <layout:basePoint1 layout:x="165" layout:y="130" />
+ <layout:basePoint2 layout:x="165" layout:y="130" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ </layout:listOfSpeciesReferenceGlyphs>
+ </layout:reactionGlyph>
+ <layout:reactionGlyph layout:id="ReactionGlyph_1" layout:reaction="Reaction_2">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="LineSegment">
+ <layout:start layout:x="235" layout:y="105" />
+ <layout:end layout:x="235" layout:y="115" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ <layout:listOfSpeciesReferenceGlyphs>
+ <layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_3" layout:role="substrate" layout:speciesGlyph="SpeciesGlyph_2" layout:speciesReference="SpeciesReference_3">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="CubicBezier">
+ <layout:start layout:x="235" layout:y="115" />
+ <layout:end layout:x="205" layout:y="160" />
+ <layout:basePoint1 layout:x="235" layout:y="130" />
+ <layout:basePoint2 layout:x="235" layout:y="130" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_4" layout:role="product" layout:speciesGlyph="SpeciesGlyph_1" layout:speciesReference="SpeciesReference_4">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="CubicBezier">
+ <layout:start layout:x="235" layout:y="105" />
+ <layout:end layout:x="205" layout:y="60" />
+ <layout:basePoint1 layout:x="235" layout:y="90" />
+ <layout:basePoint2 layout:x="235" layout:y="90" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ </layout:listOfSpeciesReferenceGlyphs>
+ </layout:reactionGlyph>
+ </layout:listOfReactionGlyphs>
+ <layout:listOfTextGlyphs>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_1" layout:id="TextGlyph_01" layout:originOfText="SpeciesGlyph_1">
+ <layout:boundingBox layout:id="bbA">
+ <layout:position layout:x="92" layout:y="26" />
+ <layout:dimensions layout:height="24" layout:width="228" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_2" layout:id="TextGlyph_02" layout:originOfText="SpeciesGlyph_2">
+ <layout:boundingBox layout:id="bbB">
+ <layout:position layout:x="92" layout:y="170" />
+ <layout:dimensions layout:height="24" layout:width="228" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ </layout:listOfTextGlyphs>
+ </layout:layout>
+ </layout:listOfLayouts>
+ <listOfUnitDefinitions>
+ <unitDefinition id="volume">
+ <listOfUnits>
+ <unit exponent="1" kind="litre" multiplier="1" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="substance">
+ <listOfUnits>
+ <unit exponent="1" kind="mole" multiplier="1" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="area">
+ <listOfUnits>
+ <unit exponent="2" kind="metre" multiplier="1" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment constant="true" id="Compartment_1" size="1" spatialDimensions="3" units="volume" />
+ </listOfCompartments>
+ <listOfSpecies>
+ <species boundaryCondition="false" compartment="Compartment_1" constant="false" hasOnlySubstanceUnits="false" id="Species_1" initialConcentration="0" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Compartment_1" constant="false" hasOnlySubstanceUnits="false" id="Species_2" initialConcentration="0" substanceUnits="substance" />
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction fast="false" id="Reaction_1" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="SpeciesReference_1" species="Species_1" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="SpeciesReference_2" species="Species_2" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="Reaction_2" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="SpeciesReference_3" species="Species_2" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="SpeciesReference_4" species="Species_1" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/converter-sbml/testFiles/layoutExample/example2.xml b/converter-sbml/testFiles/layoutExample/example2.xml
new file mode 100644
index 0000000000000000000000000000000000000000..54c1f085a9514ea97092144fc1976da11d667c1a
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/example2.xml
@@ -0,0 +1,1133 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+ <model id="Glycolysis">
+ <annotation>
+ <listOfLayouts xmlns="http://projects.eml.org/bcb/sbml/level2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <layout id="Glycolysis_Layout">
+ <dimensions width="800" height="1600"/>
+ <listOfSpeciesGlyphs>
+ <speciesGlyph id="glyph_Gluc" species="Glucose">
+ <boundingBox id="bb_01">
+ <position x="105" y="20"/>
+ <dimensions width="130" height="20"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="glyph_ATP_1" species="ATP">
+ <boundingBox id="bb_02">
+ <position x="270" y="70"/>
+ <dimensions width="80" height="20"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="glyph_ADP_1" species="ADP">
+ <boundingBox id="bb_03">
+ <position x="270" y="140"/>
+ <dimensions width="80" height="20"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="glyph_H_1" species="Hplus">
+ <boundingBox id="bb_04">
+ <position x="380" y="140"/>
+ <dimensions width="60" height="20"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="glyph_G6P" species="Glucose_6_phosphate">
+ <boundingBox id="bb_05">
+ <position x="50" y="190"/>
+ <dimensions width="270" height="20"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="glyph_F6P" species="Fructose_6_phosphate">
+ <boundingBox id="bb_06">
+ <position x="50" y="360"/>
+ <dimensions width="270" height="20"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="glyph_ATP_2" species="ATP">
+ <boundingBox id="bb_07">
+ <position x="270" y="410"/>
+ <dimensions width="80" height="20"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="glyph_ADP_2" species="ADP">
+ <boundingBox id="bb_08">
+ <position x="270" y="480"/>
+ <dimensions width="80" height="20"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="glyph_H_2" species="Hplus">
+ <boundingBox id="bb_09">
+ <position x="380" y="480"/>
+ <dimensions width="60" height="20"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="glyph_F16BP" species="Fructose_1_6_bisphosphate">
+ <boundingBox id="bb_10">
+ <position x="20" y="530"/>
+ <dimensions width="340" height="20"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="glyph_DHAP" species="Dihydroxyacetonephosphate">
+ <boundingBox id="bb_11">
+ <position x="380" y="595"/>
+ <dimensions width="340" height="20"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="glyph_GAP" species="Glyceraldehyd_3_phosphate">
+ <boundingBox id="bb_12">
+ <position x="20" y="700"/>
+ <dimensions width="340" height="20"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="glyph_NAD_1" species="NADplus">
+ <boundingBox id="bb_13">
+ <position x="270" y="750"/>
+ <dimensions width="80" height="20"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="glyph_PI_1" species="Pi">
+ <boundingBox id="bb_14">
+ <position x="380" y="750"/>
+ <dimensions width="60" height="20"/>
+ </boundingBox>
+ </speciesGlyph>
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+ <position x="390" y="480"/>
+ <dimensions width="40" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_10" graphicalObject="glyph_F16BP" originOfText="Fructose_1_6_bisphosphate">
+ <boundingBox id="bbT_10">
+ <position x="30" y="530"/>
+ <dimensions width="320" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_11" graphicalObject="glyph_DHAP" originOfText="Dihydroxyacetonephosphate">
+ <boundingBox id="bbT_11">
+ <position x="390" y="595"/>
+ <dimensions width="320" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_12" graphicalObject="glyph_GAP" originOfText="Glyceraldehyd_3_phosphate">
+ <boundingBox id="bbT_12">
+ <position x="30" y="700"/>
+ <dimensions width="320" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_13" graphicalObject="glyph_NAD_1" originOfText="NADplus">
+ <boundingBox id="bbT_13">
+ <position x="280" y="750"/>
+ <dimensions width="60" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_06" text="+">
+ <boundingBox id="bb_06">
+ <position x="350" y="750"/>
+ <dimensions width="20" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_14" graphicalObject="glyph_PI_1" originOfText="Pi">
+ <boundingBox id="bbT_14">
+ <position x="390" y="750"/>
+ <dimensions width="40" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_15" graphicalObject="glyph_NADH_1" originOfText="NADH">
+ <boundingBox id="bbT_15">
+ <position x="280" y="820"/>
+ <dimensions width="80" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_06" text="+">
+ <boundingBox id="bb_06">
+ <position x="365" y="820"/>
+ <dimensions width="20" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_16" graphicalObject="glyph_H_5" originOfText="Hplus">
+ <boundingBox id="bbT_16">
+ <position x="400" y="820"/>
+ <dimensions width="40" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_17" graphicalObject="glyph_BPG" originOfText="Bisphosphoglycerate">
+ <boundingBox id="bbT_17">
+ <position x="40" y="870"/>
+ <dimensions width="290" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_18" graphicalObject="glyph_ADP_3" originOfText="ADP">
+ <boundingBox id="bbT_18">
+ <position x="280" y="920"/>
+ <dimensions width="60" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_03" text="+">
+ <boundingBox id="bb_03">
+ <position x="350" y="920"/>
+ <dimensions width="20" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_19" graphicalObject="glyph_H_3" originOfText="Hplus">
+ <boundingBox id="bbT_19">
+ <position x="390" y="920"/>
+ <dimensions width="40" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_20" graphicalObject="glyph_ATP_3" originOfText="ATP">
+ <boundingBox id="bbT_20">
+ <position x="280" y="990"/>
+ <dimensions width="60" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_21" graphicalObject="glyph_3PG" originOfText="Phosphoglycerate3">
+ <boundingBox id="bbT_21">
+ <position x="60" y="1040"/>
+ <dimensions width="230" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_22" graphicalObject="glyph_2PG" originOfText="Phosphoglycerate2">
+ <boundingBox id="bbT_22">
+ <position x="60" y="1210"/>
+ <dimensions width="230" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_23" graphicalObject="glyph_H2O_1" originOfText="H2O">
+ <boundingBox id="bbT_23">
+ <position x="280" y="1350"/>
+ <dimensions width="60" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_24" graphicalObject="glyph_PEP" originOfText="Phosphoenolpyruvate">
+ <boundingBox id="bbT_24">
+ <position x="50" y="1380"/>
+ <dimensions width="245" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_25" graphicalObject="glyph_ADP_4" originOfText="ADP">
+ <boundingBox id="bbT_25">
+ <position x="280" y="1430"/>
+ <dimensions width="60" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_04" text="+">
+ <boundingBox id="bb_04">
+ <position x="345" y="1430"/>
+ <dimensions width="20" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_26" graphicalObject="glyph_H_4" originOfText="Hplus">
+ <boundingBox id="bbT_26">
+ <position x="380" y="1430"/>
+ <dimensions width="40" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_27" graphicalObject="glyph_ATP_4" originOfText="ATP">
+ <boundingBox id="bbT_27">
+ <position x="280" y="1520"/>
+ <dimensions width="60" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_28" graphicalObject="glyph_Pyr" originOfText="Pyruvate">
+ <boundingBox id="bbT_28">
+ <position x="110" y="1550"/>
+ <dimensions width="120" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ </listOfTextGlyphs>
+ </layout>
+ </listOfLayouts>
+ </annotation>
+ <listOfCompartments>
+ <compartment id="Yeast" size="1"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="Glucose" name="Glucose" compartment="Yeast" initialConcentration="0"/>
+ <species id="Glucose_6_phosphate" name="Glucose-6-phosphate" compartment="Yeast" initialConcentration="0"/>
+ <species id="Fructose_6_phosphate" name="Fructose-6-phosphate" compartment="Yeast" initialConcentration="0"/>
+ <species id="Fructose_1_6_bisphosphate" name="Fructose-1,6-bisphosphate" compartment="Yeast" initialConcentration="0"/>
+ <species id="Dihydroxyacetonephosphate" name="Dihydroxyacetonephosphate" compartment="Yeast" initialConcentration="0"/>
+ <species id="Glyceraldehyd_3_phosphate" name="Glyceraldehyd-3-phosphate" compartment="Yeast" initialConcentration="0"/>
+ <species id="Bisphosphoglycerate" name="1,3-Bisphosphoglycerate" compartment="Yeast" initialConcentration="0"/>
+ <species id="Phosphoglycerate3" name="3-Phosphoglycerate" compartment="Yeast" initialConcentration="0"/>
+ <species id="Phosphoglycerate2" name="2-Phosphoglycerate" compartment="Yeast" initialConcentration="0"/>
+ <species id="Phosphoenolpyruvate" name="Phosphoenolpyruvate" compartment="Yeast" initialConcentration="0"/>
+ <species id="Pyruvate" name="Pyruvate" compartment="Yeast" initialConcentration="0"/>
+ <species id="ATP" name="ATP" compartment="Yeast" initialConcentration="0"/>
+ <species id="ADP" name="ADP" compartment="Yeast" initialConcentration="0"/>
+ <species id="Hplus" name="H+" compartment="Yeast" initialConcentration="0"/>
+ <species id="NADplus" name="NAD+" compartment="Yeast" initialConcentration="0"/>
+ <species id="NADH" name="NADH" compartment="Yeast" initialConcentration="0"/>
+ <species id="H2O" name="H2O" compartment="Yeast" initialConcentration="0"/>
+ <species id="Pi" name="Pi" compartment="Yeast" initialConcentration="0"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="Hexokinase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="Glucose">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_Gluc"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="ATP">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_ATP_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Glucose_6_phosphate">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_G6P_1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="ADP">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_ADP_1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="Hplus">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_H_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="Phosphoglucoseisomerase">
+ <listOfReactants>
+ <speciesReference species="Glucose_6_phosphate">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_G6P_2"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Fructose_6_phosphate">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_F6P_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="Phosphofructokinase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="Fructose_6_phosphate">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_F6P_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="ATP">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_ATP_2"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Fructose_1_6_bisphosphate">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_F16BP_1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="ADP">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_ADP_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="Hplus">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_H_2"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="Aldolase">
+ <listOfReactants>
+ <speciesReference species="Fructose_1_6_bisphosphate">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_F16BP_2"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Dihydroxyacetonephosphate">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_DHAP_1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="Glyceraldehyd_3_phosphate">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_GAP_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="triose_phosphate_isomerase">
+ <listOfReactants>
+ <speciesReference species="Dihydroxyacetonephosphate">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_DHAP_2"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Glyceraldehyd_3_phosphate">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_GAP_2"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="GAP_Dehydrogenase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="Glyceraldehyd_3_phosphate">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_GAP_3"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="NADplus">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_NAD_1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="Pi">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_PI_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Bisphosphoglycerate">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_BPG_1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="NADH">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_NADH_1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="Hplus">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_H_5"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="Phosphoglyceratekinase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="Bisphosphoglycerate">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_BPG_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="ADP">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_ADP_3"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="Hplus">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_H_3"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Phosphoglycerate3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_3PG_1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="ATP">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_ATP_3"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="Phosphoglyceratemutase">
+ <listOfReactants>
+ <speciesReference species="Phosphoglycerate3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_3PG_2"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Phosphoglycerate2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_2PG_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="Enolase">
+ <listOfReactants>
+ <speciesReference species="Phosphoglycerate3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_2PG_2"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Phosphoglycerate2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_PEP_1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="H2O">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_H2O_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="Pyruvatekinase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="Phosphoglycerate3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_PEP_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="ADP">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_ADP_4"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="Hplus">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_H_4"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Phosphoglycerate2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_Pyr_1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="ATP">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ref_ATP_4"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/converter-sbml/testFiles/layoutExample/example2_level3.xml b/converter-sbml/testFiles/layoutExample/example2_level3.xml
new file mode 100644
index 0000000000000000000000000000000000000000..7769bfe7421436e860409bea29418882067cbfe2
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/example2_level3.xml
@@ -0,0 +1,1005 @@
+<?xml version='1.0' encoding='utf-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" layout:required="false" level="3" version="1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+ <model areaUnits="area" extentUnits="substance" id="Glycolysis" lengthUnits="metre" substanceUnits="substance" timeUnits="second" volumeUnits="volume">
+ <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <layout:layout layout:id="Glycolysis_Layout">
+ <layout:dimensions layout:height="1600" layout:width="800" />
+ <layout:listOfSpeciesGlyphs>
+ <layout:speciesGlyph layout:id="glyph_Gluc" layout:species="Glucose">
+ <layout:boundingBox layout:id="bb_01">
+ <layout:position layout:x="105" layout:y="20" />
+ <layout:dimensions layout:height="20" layout:width="130" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="glyph_ATP_1" layout:species="ATP">
+ <layout:boundingBox layout:id="bb_02">
+ <layout:position layout:x="270" layout:y="70" />
+ <layout:dimensions layout:height="20" layout:width="80" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="glyph_ADP_1" layout:species="ADP">
+ <layout:boundingBox layout:id="bb_03">
+ <layout:position layout:x="270" layout:y="140" />
+ <layout:dimensions layout:height="20" layout:width="80" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="glyph_H_1" layout:species="Hplus">
+ <layout:boundingBox layout:id="bb_04">
+ <layout:position layout:x="380" layout:y="140" />
+ <layout:dimensions layout:height="20" layout:width="60" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="glyph_G6P" layout:species="Glucose_6_phosphate">
+ <layout:boundingBox layout:id="bb_05">
+ <layout:position layout:x="50" layout:y="190" />
+ <layout:dimensions layout:height="20" layout:width="270" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="glyph_F6P" layout:species="Fructose_6_phosphate">
+ <layout:boundingBox layout:id="bb_06">
+ <layout:position layout:x="50" layout:y="360" />
+ <layout:dimensions layout:height="20" layout:width="270" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="glyph_ATP_2" layout:species="ATP">
+ <layout:boundingBox layout:id="bb_07">
+ <layout:position layout:x="270" layout:y="410" />
+ <layout:dimensions layout:height="20" layout:width="80" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="glyph_ADP_2" layout:species="ADP">
+ <layout:boundingBox layout:id="bb_08">
+ <layout:position layout:x="270" layout:y="480" />
+ <layout:dimensions layout:height="20" layout:width="80" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="glyph_H_2" layout:species="Hplus">
+ <layout:boundingBox layout:id="bb_09">
+ <layout:position layout:x="380" layout:y="480" />
+ <layout:dimensions layout:height="20" layout:width="60" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="glyph_F16BP" layout:species="Fructose_1_6_bisphosphate">
+ <layout:boundingBox layout:id="bb_10">
+ <layout:position layout:x="20" layout:y="530" />
+ <layout:dimensions layout:height="20" layout:width="340" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="glyph_DHAP" layout:species="Dihydroxyacetonephosphate">
+ <layout:boundingBox layout:id="bb_11">
+ <layout:position layout:x="380" layout:y="595" />
+ <layout:dimensions layout:height="20" layout:width="340" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="glyph_GAP" layout:species="Glyceraldehyd_3_phosphate">
+ <layout:boundingBox layout:id="bb_12">
+ <layout:position layout:x="20" layout:y="700" />
+ <layout:dimensions layout:height="20" layout:width="340" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="glyph_NAD_1" layout:species="NADplus">
+ <layout:boundingBox layout:id="bb_13">
+ <layout:position layout:x="270" layout:y="750" />
+ <layout:dimensions layout:height="20" layout:width="80" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="glyph_PI_1" layout:species="Pi">
+ <layout:boundingBox layout:id="bb_14">
+ <layout:position layout:x="380" layout:y="750" />
+ <layout:dimensions layout:height="20" layout:width="60" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="glyph_NADH_1" layout:species="NADH">
+ <layout:boundingBox layout:id="bb_15">
+ <layout:position layout:x="270" layout:y="820" />
+ <layout:dimensions layout:height="20" layout:width="100" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="glyph_H_5" layout:species="Hplus">
+ <layout:boundingBox layout:id="bb_16">
+ <layout:position layout:x="390" layout:y="820" />
+ <layout:dimensions layout:height="20" layout:width="60" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="glyph_BPG" layout:species="Bisphosphoglycerate">
+ <layout:boundingBox layout:id="bb_17">
+ <layout:position layout:x="30" layout:y="870" />
+ <layout:dimensions layout:height="20" layout:width="310" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="glyph_ADP_3" layout:species="ADP">
+ <layout:boundingBox layout:id="bb_18">
+ <layout:position layout:x="270" layout:y="920" />
+ <layout:dimensions layout:height="20" layout:width="80" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
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+ </layout:listOfCurveSegments>
+ </layout:curve>
+ <layout:listOfSpeciesReferenceGlyphs>
+ <layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_09" layout:role="substrate" layout:speciesGlyph="glyph_PEP" layout:speciesReference="ref_PEP_2">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="LineSegment">
+ <layout:start layout:x="170" layout:y="1460" />
+ <layout:end layout:x="170" layout:y="1410" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_20" layout:role="product" layout:speciesGlyph="glyph_Pyr" layout:speciesReference="ref_Pyr_1">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="LineSegment">
+ <layout:start layout:x="170" layout:y="1490" />
+ <layout:end layout:x="170" layout:y="1540" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_30" layout:role="sidesubstrate" layout:speciesGlyph="glyph_ADP_4" layout:speciesReference="ref_ADP_4">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="CubicBezier">
+ <layout:start layout:x="170" layout:y="1460" />
+ <layout:end layout:x="260" layout:y="1440" />
+ <layout:basePoint1 layout:x="170" layout:y="1440" />
+ <layout:basePoint2 layout:x="170" layout:y="1440" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_31" layout:role="sideproduct" layout:speciesGlyph="glyph_ATP_4" layout:speciesReference="ref_ATP_4">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="CubicBezier">
+ <layout:start layout:x="170" layout:y="1490" />
+ <layout:end layout:x="260" layout:y="1530" />
+ <layout:basePoint1 layout:x="170" layout:y="1530" />
+ <layout:basePoint2 layout:x="170" layout:y="1530" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ </layout:listOfSpeciesReferenceGlyphs>
+ </layout:reactionGlyph>
+ </layout:listOfReactionGlyphs>
+ <layout:listOfTextGlyphs>
+ <layout:textGlyph layout:graphicalObject="glyph_Gluc" layout:id="TextGlyph_01" layout:originOfText="Glucose">
+ <layout:boundingBox layout:id="bbT_01">
+ <layout:position layout:x="115" layout:y="20" />
+ <layout:dimensions layout:height="20" layout:width="110" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_ATP_1" layout:id="TextGlyph_02" layout:originOfText="ATP">
+ <layout:boundingBox layout:id="bbT_02">
+ <layout:position layout:x="280" layout:y="70" />
+ <layout:dimensions layout:height="20" layout:width="60" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_ADP_1" layout:id="TextGlyph_03" layout:originOfText="ADP">
+ <layout:boundingBox layout:id="bbT_03">
+ <layout:position layout:x="280" layout:y="140" />
+ <layout:dimensions layout:height="20" layout:width="60" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:id="TextGlyph_01" layout:text="+">
+ <layout:boundingBox layout:id="bb_01">
+ <layout:position layout:x="350" layout:y="140" />
+ <layout:dimensions layout:height="20" layout:width="20" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_H_1" layout:id="TextGlyph_04" layout:originOfText="Hplus">
+ <layout:boundingBox layout:id="bbT_04">
+ <layout:position layout:x="390" layout:y="140" />
+ <layout:dimensions layout:height="20" layout:width="40" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_G6P" layout:id="TextGlyph_05" layout:originOfText="Glucose_6_phosphate">
+ <layout:boundingBox layout:id="bbT_05">
+ <layout:position layout:x="60" layout:y="190" />
+ <layout:dimensions layout:height="20" layout:width="250" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_F6P" layout:id="TextGlyph_06" layout:originOfText="Fructose_6_phosphate">
+ <layout:boundingBox layout:id="bbT_06">
+ <layout:position layout:x="60" layout:y="360" />
+ <layout:dimensions layout:height="20" layout:width="250" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_ATP_2" layout:id="TextGlyph_07" layout:originOfText="ATP">
+ <layout:boundingBox layout:id="bbT_07">
+ <layout:position layout:x="280" layout:y="410" />
+ <layout:dimensions layout:height="20" layout:width="60" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_ADP_2" layout:id="TextGlyph_08" layout:originOfText="ADP">
+ <layout:boundingBox layout:id="bbT_08">
+ <layout:position layout:x="280" layout:y="480" />
+ <layout:dimensions layout:height="20" layout:width="60" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:id="TextGlyph_02" layout:text="+">
+ <layout:boundingBox layout:id="bb_02">
+ <layout:position layout:x="350" layout:y="480" />
+ <layout:dimensions layout:height="20" layout:width="20" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_H_2" layout:id="TextGlyph_09" layout:originOfText="Hplus">
+ <layout:boundingBox layout:id="bbT_09">
+ <layout:position layout:x="390" layout:y="480" />
+ <layout:dimensions layout:height="20" layout:width="40" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_F16BP" layout:id="TextGlyph_10" layout:originOfText="Fructose_1_6_bisphosphate">
+ <layout:boundingBox layout:id="bbT_10">
+ <layout:position layout:x="30" layout:y="530" />
+ <layout:dimensions layout:height="20" layout:width="320" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_DHAP" layout:id="TextGlyph_11" layout:originOfText="Dihydroxyacetonephosphate">
+ <layout:boundingBox layout:id="bbT_11">
+ <layout:position layout:x="390" layout:y="595" />
+ <layout:dimensions layout:height="20" layout:width="320" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_GAP" layout:id="TextGlyph_12" layout:originOfText="Glyceraldehyd_3_phosphate">
+ <layout:boundingBox layout:id="bbT_12">
+ <layout:position layout:x="30" layout:y="700" />
+ <layout:dimensions layout:height="20" layout:width="320" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_NAD_1" layout:id="TextGlyph_13" layout:originOfText="NADplus">
+ <layout:boundingBox layout:id="bbT_13">
+ <layout:position layout:x="280" layout:y="750" />
+ <layout:dimensions layout:height="20" layout:width="60" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:id="TextGlyph_06" layout:text="+">
+ <layout:boundingBox layout:id="bb_06">
+ <layout:position layout:x="350" layout:y="750" />
+ <layout:dimensions layout:height="20" layout:width="20" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_PI_1" layout:id="TextGlyph_14" layout:originOfText="Pi">
+ <layout:boundingBox layout:id="bbT_14">
+ <layout:position layout:x="390" layout:y="750" />
+ <layout:dimensions layout:height="20" layout:width="40" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_NADH_1" layout:id="TextGlyph_15" layout:originOfText="NADH">
+ <layout:boundingBox layout:id="bbT_15">
+ <layout:position layout:x="280" layout:y="820" />
+ <layout:dimensions layout:height="20" layout:width="80" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:id="TextGlyph_06" layout:text="+">
+ <layout:boundingBox layout:id="bb_06">
+ <layout:position layout:x="365" layout:y="820" />
+ <layout:dimensions layout:height="20" layout:width="20" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_H_5" layout:id="TextGlyph_16" layout:originOfText="Hplus">
+ <layout:boundingBox layout:id="bbT_16">
+ <layout:position layout:x="400" layout:y="820" />
+ <layout:dimensions layout:height="20" layout:width="40" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_BPG" layout:id="TextGlyph_17" layout:originOfText="Bisphosphoglycerate">
+ <layout:boundingBox layout:id="bbT_17">
+ <layout:position layout:x="40" layout:y="870" />
+ <layout:dimensions layout:height="20" layout:width="290" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_ADP_3" layout:id="TextGlyph_18" layout:originOfText="ADP">
+ <layout:boundingBox layout:id="bbT_18">
+ <layout:position layout:x="280" layout:y="920" />
+ <layout:dimensions layout:height="20" layout:width="60" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:id="TextGlyph_03" layout:text="+">
+ <layout:boundingBox layout:id="bb_03">
+ <layout:position layout:x="350" layout:y="920" />
+ <layout:dimensions layout:height="20" layout:width="20" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_H_3" layout:id="TextGlyph_19" layout:originOfText="Hplus">
+ <layout:boundingBox layout:id="bbT_19">
+ <layout:position layout:x="390" layout:y="920" />
+ <layout:dimensions layout:height="20" layout:width="40" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_ATP_3" layout:id="TextGlyph_20" layout:originOfText="ATP">
+ <layout:boundingBox layout:id="bbT_20">
+ <layout:position layout:x="280" layout:y="990" />
+ <layout:dimensions layout:height="20" layout:width="60" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_3PG" layout:id="TextGlyph_21" layout:originOfText="Phosphoglycerate3">
+ <layout:boundingBox layout:id="bbT_21">
+ <layout:position layout:x="60" layout:y="1040" />
+ <layout:dimensions layout:height="20" layout:width="230" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_2PG" layout:id="TextGlyph_22" layout:originOfText="Phosphoglycerate2">
+ <layout:boundingBox layout:id="bbT_22">
+ <layout:position layout:x="60" layout:y="1210" />
+ <layout:dimensions layout:height="20" layout:width="230" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_H2O_1" layout:id="TextGlyph_23" layout:originOfText="H2O">
+ <layout:boundingBox layout:id="bbT_23">
+ <layout:position layout:x="280" layout:y="1350" />
+ <layout:dimensions layout:height="20" layout:width="60" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_PEP" layout:id="TextGlyph_24" layout:originOfText="Phosphoenolpyruvate">
+ <layout:boundingBox layout:id="bbT_24">
+ <layout:position layout:x="50" layout:y="1380" />
+ <layout:dimensions layout:height="20" layout:width="245" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_ADP_4" layout:id="TextGlyph_25" layout:originOfText="ADP">
+ <layout:boundingBox layout:id="bbT_25">
+ <layout:position layout:x="280" layout:y="1430" />
+ <layout:dimensions layout:height="20" layout:width="60" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:id="TextGlyph_04" layout:text="+">
+ <layout:boundingBox layout:id="bb_04">
+ <layout:position layout:x="345" layout:y="1430" />
+ <layout:dimensions layout:height="20" layout:width="20" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_H_4" layout:id="TextGlyph_26" layout:originOfText="Hplus">
+ <layout:boundingBox layout:id="bbT_26">
+ <layout:position layout:x="380" layout:y="1430" />
+ <layout:dimensions layout:height="20" layout:width="40" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_ATP_4" layout:id="TextGlyph_27" layout:originOfText="ATP">
+ <layout:boundingBox layout:id="bbT_27">
+ <layout:position layout:x="280" layout:y="1520" />
+ <layout:dimensions layout:height="20" layout:width="60" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_Pyr" layout:id="TextGlyph_28" layout:originOfText="Pyruvate">
+ <layout:boundingBox layout:id="bbT_28">
+ <layout:position layout:x="110" layout:y="1550" />
+ <layout:dimensions layout:height="20" layout:width="120" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ </layout:listOfTextGlyphs>
+ </layout:layout>
+ </layout:listOfLayouts>
+ <listOfUnitDefinitions>
+ <unitDefinition id="volume">
+ <listOfUnits>
+ <unit exponent="1" kind="litre" multiplier="1" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="substance">
+ <listOfUnits>
+ <unit exponent="1" kind="mole" multiplier="1" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="area">
+ <listOfUnits>
+ <unit exponent="2" kind="metre" multiplier="1" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment constant="true" id="Yeast" size="1" spatialDimensions="3" units="volume" />
+ </listOfCompartments>
+ <listOfSpecies>
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="Glucose" initialConcentration="0" name="Glucose" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="Glucose_6_phosphate" initialConcentration="0" name="Glucose-6-phosphate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="Fructose_6_phosphate" initialConcentration="0" name="Fructose-6-phosphate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="Fructose_1_6_bisphosphate" initialConcentration="0" name="Fructose-1,6-bisphosphate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="Dihydroxyacetonephosphate" initialConcentration="0" name="Dihydroxyacetonephosphate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="Glyceraldehyd_3_phosphate" initialConcentration="0" name="Glyceraldehyd-3-phosphate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="Bisphosphoglycerate" initialConcentration="0" name="1,3-Bisphosphoglycerate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="Phosphoglycerate3" initialConcentration="0" name="3-Phosphoglycerate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="Phosphoglycerate2" initialConcentration="0" name="2-Phosphoglycerate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="Phosphoenolpyruvate" initialConcentration="0" name="Phosphoenolpyruvate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="Pyruvate" initialConcentration="0" name="Pyruvate" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="ATP" initialConcentration="0" name="ATP" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="ADP" initialConcentration="0" name="ADP" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="Hplus" initialConcentration="0" name="H+" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="NADplus" initialConcentration="0" name="NAD+" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="NADH" initialConcentration="0" name="NADH" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="H2O" initialConcentration="0" name="H2O" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="Pi" initialConcentration="0" name="Pi" substanceUnits="substance" />
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction fast="false" id="Hexokinase" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="ref_Gluc" species="Glucose" stoichiometry="1" />
+ <speciesReference constant="true" id="ref_ATP_1" species="ATP" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="ref_G6P_1" species="Glucose_6_phosphate" stoichiometry="1" />
+ <speciesReference constant="true" id="ref_ADP_1" species="ADP" stoichiometry="1" />
+ <speciesReference constant="true" id="ref_H_1" species="Hplus" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="Phosphoglucoseisomerase" reversible="true">
+ <listOfReactants>
+ <speciesReference constant="true" id="ref_G6P_2" species="Glucose_6_phosphate" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="ref_F6P_1" species="Fructose_6_phosphate" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="Phosphofructokinase" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="ref_F6P_2" species="Fructose_6_phosphate" stoichiometry="1" />
+ <speciesReference constant="true" id="ref_ATP_2" species="ATP" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="ref_F16BP_1" species="Fructose_1_6_bisphosphate" stoichiometry="1" />
+ <speciesReference constant="true" id="ref_ADP_2" species="ADP" stoichiometry="1" />
+ <speciesReference constant="true" id="ref_H_2" species="Hplus" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="Aldolase" reversible="true">
+ <listOfReactants>
+ <speciesReference constant="true" id="ref_F16BP_2" species="Fructose_1_6_bisphosphate" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="ref_DHAP_1" species="Dihydroxyacetonephosphate" stoichiometry="1" />
+ <speciesReference constant="true" id="ref_GAP_1" species="Glyceraldehyd_3_phosphate" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="triose_phosphate_isomerase" reversible="true">
+ <listOfReactants>
+ <speciesReference constant="true" id="ref_DHAP_2" species="Dihydroxyacetonephosphate" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="ref_GAP_2" species="Glyceraldehyd_3_phosphate" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="GAP_Dehydrogenase" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="ref_GAP_3" species="Glyceraldehyd_3_phosphate" stoichiometry="1" />
+ <speciesReference constant="true" id="ref_NAD_1" species="NADplus" stoichiometry="1" />
+ <speciesReference constant="true" id="ref_PI_1" species="Pi" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="ref_BPG_1" species="Bisphosphoglycerate" stoichiometry="1" />
+ <speciesReference constant="true" id="ref_NADH_1" species="NADH" stoichiometry="1" />
+ <speciesReference constant="true" id="ref_H_5" species="Hplus" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="Phosphoglyceratekinase" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="ref_BPG_2" species="Bisphosphoglycerate" stoichiometry="1" />
+ <speciesReference constant="true" id="ref_ADP_3" species="ADP" stoichiometry="1" />
+ <speciesReference constant="true" id="ref_H_3" species="Hplus" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="ref_3PG_1" species="Phosphoglycerate3" stoichiometry="1" />
+ <speciesReference constant="true" id="ref_ATP_3" species="ATP" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="Phosphoglyceratemutase" reversible="true">
+ <listOfReactants>
+ <speciesReference constant="true" id="ref_3PG_2" species="Phosphoglycerate3" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="ref_2PG_1" species="Phosphoglycerate2" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="Enolase" reversible="true">
+ <listOfReactants>
+ <speciesReference constant="true" id="ref_2PG_2" species="Phosphoglycerate3" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="ref_PEP_1" species="Phosphoglycerate2" stoichiometry="1" />
+ <speciesReference constant="true" id="ref_H2O_1" species="H2O" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="Pyruvatekinase" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="ref_PEP_2" species="Phosphoglycerate3" stoichiometry="1" />
+ <speciesReference constant="true" id="ref_ADP_4" species="ADP" stoichiometry="1" />
+ <speciesReference constant="true" id="ref_H_4" species="Hplus" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="ref_Pyr_1" species="Phosphoglycerate2" stoichiometry="1" />
+ <speciesReference constant="true" id="ref_ATP_4" species="ATP" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/converter-sbml/testFiles/layoutExample/example3.xml b/converter-sbml/testFiles/layoutExample/example3.xml
new file mode 100644
index 0000000000000000000000000000000000000000..f4b4da53e49a944afa0299ae2a8ff93a8e839899
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/example3.xml
@@ -0,0 +1,216 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+ <model id="TestModel_with_modifiers">
+ <annotation>
+ <listOfLayouts xmlns="http://projects.eml.org/bcb/sbml/level2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <layout id="Layout_1">
+ <dimensions width="400" height="230"/>
+ <listOfCompartmentGlyphs>
+ <compartmentGlyph id="CompartmentGlyph_1" compartment="Yeast">
+ <boundingBox id="bb1">
+ <position x="5" y="5"/>
+ <dimensions width="390" height="220"/>
+ </boundingBox>
+ </compartmentGlyph>
+ </listOfCompartmentGlyphs>
+ <listOfSpeciesGlyphs>
+ <speciesGlyph id="SpeciesGlyph_Glucose" species="Glucose">
+ <boundingBox id="bb2">
+ <position x="105" y="20"/>
+ <dimensions width="130" height="20"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_G6P" species="Glucose_6_phosphate">
+ <boundingBox id="bb5">
+ <position x="50" y="190"/>
+ <dimensions width="270" height="20"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_ATP" species="ATP">
+ <boundingBox id="bb3">
+ <position x="270" y="70"/>
+ <dimensions width="80" height="20"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="glyph_ADP" species="ADP">
+ <boundingBox id="bb4">
+ <position x="270" y="140"/>
+ <dimensions width="80" height="20"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_Pi" species="Pi">
+ <boundingBox id="bb6">
+ <position x="50" y="100"/>
+ <dimensions width="60" height="20"/>
+ </boundingBox>
+ </speciesGlyph>
+ </listOfSpeciesGlyphs>
+ <listOfReactionGlyphs>
+ <reactionGlyph id="glyph_Hexokinase" reaction="Hexokinase">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
+ <start x="170" y="100"/>
+ <end x="170" y="130"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ <listOfSpeciesReferenceGlyphs>
+ <speciesReferenceGlyph id="SpeciesReferenceGlyph_Glucose" speciesReference="SpeciesReference_Glucose" speciesGlyph="SpeciesGlyph_Glucose" role="substrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
+ <start x="170" y="100"/>
+ <end x="170" y="50"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="SpeciesReferenceGlyph_ATP" speciesReference="SpeciesReference_ATP" speciesGlyph="SpeciesGlyph_ATP" role="sidesubstrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
+ <start x="170" y="100"/>
+ <end x="260" y="80"/>
+ <basePoint1 x="170" y="80"/>
+ <basePoint2 x="170" y="80"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="SpeciesReferenceGlyph_G6P_1" speciesReference="SpeciesReference_G6P" speciesGlyph="SpeciesGlyph_G6P" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
+ <start x="170" y="130"/>
+ <end x="170" y="180"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="SpeciesReferenceGlyph_ADP" speciesReference="SpeciesReference_ADP" speciesGlyph="glyph_ADP" role="sideproduct">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
+ <start x="170" y="130"/>
+ <end x="260" y="150"/>
+ <basePoint1 x="170" y="150"/>
+ <basePoint2 x="170" y="150"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="SpeciesReferenceGlyph_G6P_2" speciesReference="ModifierSpeciesReference_G6P" speciesGlyph="SpeciesGlyph_G6P" role="inhibitor">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
+ <start x="45" y="200"/>
+ <end x="165" y="120"/>
+ <basePoint1 x="0" y="200"/>
+ <basePoint2 x="0" y="120"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="SpeciesReferenceGlyph_PI" speciesReference="ModifierSpeciesReference_Pi" speciesGlyph="SpeciesGlyph_Pi" role="activator">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
+ <start x="115" y="110"/>
+ <end x="165" y="110"/>
+ <basePoint1 x="140" y="110"/>
+ <basePoint2 x="140" y="110"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ </listOfSpeciesReferenceGlyphs>
+ </reactionGlyph>
+ </listOfReactionGlyphs>
+ <listOfTextGlyphs>
+ <textGlyph id="TextGlyph_Glucose" graphicalObject="SpeciesGlyph_Glucose" originOfText="Glucose">
+ <boundingBox id="bbA">
+ <position x="115" y="20"/>
+ <dimensions width="110" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_G6P" graphicalObject="SpeciesGlyph_G6P" originOfText="Glucose_6_phosphate">
+ <boundingBox id="bbD">
+ <position x="60" y="190"/>
+ <dimensions width="250" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_ATP" graphicalObject="SpeciesGlyph_ATP" originOfText="ATP">
+ <boundingBox id="bbB">
+ <position x="280" y="70"/>
+ <dimensions width="60" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_ADP" graphicalObject="glyph_ADP" originOfText="ADP">
+ <boundingBox id="bbC">
+ <position x="280" y="140"/>
+ <dimensions width="60" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_PI" graphicalObject="SpeciesGlyph_Pi" originOfText="Pi">
+ <boundingBox id="bbE">
+ <position x="60" y="100"/>
+ <dimensions width="40" height="20"/>
+ </boundingBox>
+ </textGlyph>
+ </listOfTextGlyphs>
+ </layout>
+ </listOfLayouts>
+ </annotation>
+ <listOfCompartments>
+ <compartment id="Yeast" size="1"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="Glucose" compartment="Yeast" initialConcentration="0"/>
+ <species id="Glucose_6_phosphate" compartment="Yeast" initialConcentration="0"/>
+ <species id="ATP" compartment="Yeast" initialConcentration="0"/>
+ <species id="ADP" compartment="Yeast" initialConcentration="0"/>
+ <species id="Pi" compartment="Yeast" initialConcentration="0"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="Hexokinase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="Glucose">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="SpeciesReference_Glucose"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="ATP">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="SpeciesReference_ATP"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Glucose_6_phosphate">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="SpeciesReference_G6P"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="ADP">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="SpeciesReference_ADP"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ <listOfModifiers>
+ <modifierSpeciesReference species="Glucose_6_phosphate">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ModifierSpeciesReference_G6P"/>
+ </annotation>
+ </modifierSpeciesReference>
+ <modifierSpeciesReference species="Pi">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="ModifierSpeciesReference_Pi"/>
+ </annotation>
+ </modifierSpeciesReference>
+ </listOfModifiers>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/converter-sbml/testFiles/layoutExample/example3_level3.xml b/converter-sbml/testFiles/layoutExample/example3_level3.xml
new file mode 100644
index 0000000000000000000000000000000000000000..b36d6cb6f7d9b93adcf77cdbb227c73260b07189
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/example3_level3.xml
@@ -0,0 +1,209 @@
+<?xml version='1.0' encoding='utf-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" layout:required="false" level="3" version="1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+ <model areaUnits="area" extentUnits="substance" id="TestModel_with_modifiers" lengthUnits="metre" substanceUnits="substance" timeUnits="second" volumeUnits="volume">
+ <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <layout:layout layout:id="Layout_1">
+ <layout:dimensions layout:height="230" layout:width="400" />
+ <layout:listOfCompartmentGlyphs>
+ <layout:compartmentGlyph layout:compartment="Yeast" layout:id="CompartmentGlyph_1">
+ <layout:boundingBox layout:id="bb1">
+ <layout:position layout:x="5" layout:y="5" />
+ <layout:dimensions layout:height="220" layout:width="390" />
+ </layout:boundingBox>
+ </layout:compartmentGlyph>
+ </layout:listOfCompartmentGlyphs>
+ <layout:listOfSpeciesGlyphs>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_Glucose" layout:species="Glucose">
+ <layout:boundingBox layout:id="bb2">
+ <layout:position layout:x="105" layout:y="20" />
+ <layout:dimensions layout:height="20" layout:width="130" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_G6P" layout:species="Glucose_6_phosphate">
+ <layout:boundingBox layout:id="bb5">
+ <layout:position layout:x="50" layout:y="190" />
+ <layout:dimensions layout:height="20" layout:width="270" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_ATP" layout:species="ATP">
+ <layout:boundingBox layout:id="bb3">
+ <layout:position layout:x="270" layout:y="70" />
+ <layout:dimensions layout:height="20" layout:width="80" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="glyph_ADP" layout:species="ADP">
+ <layout:boundingBox layout:id="bb4">
+ <layout:position layout:x="270" layout:y="140" />
+ <layout:dimensions layout:height="20" layout:width="80" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_Pi" layout:species="Pi">
+ <layout:boundingBox layout:id="bb6">
+ <layout:position layout:x="50" layout:y="100" />
+ <layout:dimensions layout:height="20" layout:width="60" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ </layout:listOfSpeciesGlyphs>
+ <layout:listOfReactionGlyphs>
+ <layout:reactionGlyph layout:id="glyph_Hexokinase" layout:reaction="Hexokinase">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="LineSegment">
+ <layout:start layout:x="170" layout:y="100" />
+ <layout:end layout:x="170" layout:y="130" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ <layout:listOfSpeciesReferenceGlyphs>
+ <layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_Glucose" layout:role="substrate" layout:speciesGlyph="SpeciesGlyph_Glucose"
+ layout:speciesReference="SpeciesReference_Glucose">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="LineSegment">
+ <layout:start layout:x="170" layout:y="100" />
+ <layout:end layout:x="170" layout:y="50" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_ATP" layout:role="sidesubstrate" layout:speciesGlyph="SpeciesGlyph_ATP" layout:speciesReference="SpeciesReference_ATP">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="CubicBezier">
+ <layout:start layout:x="170" layout:y="100" />
+ <layout:end layout:x="260" layout:y="80" />
+ <layout:basePoint1 layout:x="170" layout:y="80" />
+ <layout:basePoint2 layout:x="170" layout:y="80" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_G6P_1" layout:role="product" layout:speciesGlyph="SpeciesGlyph_G6P" layout:speciesReference="SpeciesReference_G6P">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="LineSegment">
+ <layout:start layout:x="170" layout:y="130" />
+ <layout:end layout:x="170" layout:y="180" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_ADP" layout:role="sideproduct" layout:speciesGlyph="glyph_ADP" layout:speciesReference="SpeciesReference_ADP">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="CubicBezier">
+ <layout:start layout:x="170" layout:y="130" />
+ <layout:end layout:x="260" layout:y="150" />
+ <layout:basePoint1 layout:x="170" layout:y="150" />
+ <layout:basePoint2 layout:x="170" layout:y="150" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_G6P_2" layout:role="inhibitor" layout:speciesGlyph="SpeciesGlyph_G6P"
+ layout:speciesReference="ModifierSpeciesReference_G6P">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="CubicBezier">
+ <layout:start layout:x="45" layout:y="200" />
+ <layout:end layout:x="165" layout:y="120" />
+ <layout:basePoint1 layout:x="0" layout:y="200" />
+ <layout:basePoint2 layout:x="0" layout:y="120" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_PI" layout:role="activator" layout:speciesGlyph="SpeciesGlyph_Pi" layout:speciesReference="ModifierSpeciesReference_Pi">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="CubicBezier">
+ <layout:start layout:x="115" layout:y="110" />
+ <layout:end layout:x="165" layout:y="110" />
+ <layout:basePoint1 layout:x="140" layout:y="110" />
+ <layout:basePoint2 layout:x="140" layout:y="110" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ </layout:listOfSpeciesReferenceGlyphs>
+ </layout:reactionGlyph>
+ </layout:listOfReactionGlyphs>
+ <layout:listOfTextGlyphs>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_Glucose" layout:id="TextGlyph_Glucose" layout:originOfText="Glucose">
+ <layout:boundingBox layout:id="bbA">
+ <layout:position layout:x="115" layout:y="20" />
+ <layout:dimensions layout:height="20" layout:width="110" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_G6P" layout:id="TextGlyph_G6P" layout:originOfText="Glucose_6_phosphate">
+ <layout:boundingBox layout:id="bbD">
+ <layout:position layout:x="60" layout:y="190" />
+ <layout:dimensions layout:height="20" layout:width="250" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_ATP" layout:id="TextGlyph_ATP" layout:originOfText="ATP">
+ <layout:boundingBox layout:id="bbB">
+ <layout:position layout:x="280" layout:y="70" />
+ <layout:dimensions layout:height="20" layout:width="60" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="glyph_ADP" layout:id="TextGlyph_ADP" layout:originOfText="ADP">
+ <layout:boundingBox layout:id="bbC">
+ <layout:position layout:x="280" layout:y="140" />
+ <layout:dimensions layout:height="20" layout:width="60" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_Pi" layout:id="TextGlyph_PI" layout:originOfText="Pi">
+ <layout:boundingBox layout:id="bbE">
+ <layout:position layout:x="60" layout:y="100" />
+ <layout:dimensions layout:height="20" layout:width="40" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ </layout:listOfTextGlyphs>
+ </layout:layout>
+ </layout:listOfLayouts>
+ <listOfUnitDefinitions>
+ <unitDefinition id="volume">
+ <listOfUnits>
+ <unit exponent="1" kind="litre" multiplier="1" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="substance">
+ <listOfUnits>
+ <unit exponent="1" kind="mole" multiplier="1" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="area">
+ <listOfUnits>
+ <unit exponent="2" kind="metre" multiplier="1" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment constant="true" id="Yeast" size="1" spatialDimensions="3" units="volume" />
+ </listOfCompartments>
+ <listOfSpecies>
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="Glucose" initialConcentration="0" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="Glucose_6_phosphate" initialConcentration="0" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="ATP" initialConcentration="0" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="ADP" initialConcentration="0" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Yeast" constant="false" hasOnlySubstanceUnits="false" id="Pi" initialConcentration="0" substanceUnits="substance" />
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction fast="false" id="Hexokinase" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="SpeciesReference_Glucose" species="Glucose" stoichiometry="1" />
+ <speciesReference constant="true" id="SpeciesReference_ATP" species="ATP" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="SpeciesReference_G6P" species="Glucose_6_phosphate" stoichiometry="1" />
+ <speciesReference constant="true" id="SpeciesReference_ADP" species="ADP" stoichiometry="1" />
+ </listOfProducts>
+ <listOfModifiers>
+ <modifierSpeciesReference id="ModifierSpeciesReference_G6P" species="Glucose_6_phosphate" />
+ <modifierSpeciesReference id="ModifierSpeciesReference_Pi" species="Pi" />
+ </listOfModifiers>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/converter-sbml/testFiles/layoutExample/example4.xml b/converter-sbml/testFiles/layoutExample/example4.xml
new file mode 100644
index 0000000000000000000000000000000000000000..320dca7c0c9d52f7fc8a4c7f412c3a5ae4fb8104
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/example4.xml
@@ -0,0 +1,1024 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+ <model id="TestModel">
+ <annotation>
+ <listOfLayouts xmlns="http://projects.eml.org/bcb/sbml/level2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <layout id="Layout_1">
+ <dimensions width="2300" height="1000"/>
+ <listOfCompartmentGlyphs>
+ <compartmentGlyph id="CompartmentGlyph_1" compartment="Hepatocyte">
+ <boundingBox id="bb_compartment">
+ <position x="10" y="10"/>
+ <dimensions width="1380" height="980"/>
+ </boundingBox>
+ </compartmentGlyph>
+ <compartmentGlyph id="Mito1_Glyph" compartment="Mito_1">
+ <boundingBox id="bb_mito1">
+ <position x="100" y="100"/>
+ <dimensions width="300" height="100"/>
+ </boundingBox>
+ </compartmentGlyph>
+ <compartmentGlyph id="Mito2_Glyph" compartment="Mito_2">
+ <boundingBox id="bb_mito2">
+ <position x="200" y="650"/>
+ <dimensions width="300" height="100"/>
+ </boundingBox>
+ </compartmentGlyph>
+ <compartmentGlyph id="Mito3_Glyph" compartment="Mito_3">
+ <boundingBox id="bb_mito3">
+ <position x="1000" y="800"/>
+ <dimensions width="300" height="100"/>
+ </boundingBox>
+ </compartmentGlyph>
+ </listOfCompartmentGlyphs>
+ <listOfSpeciesGlyphs>
+ <speciesGlyph id="SpeciesGlyph_malate_cyt" species="malate_cyt">
+ <boundingBox id="bb_sg_malate_cyt">
+ <position x="580" y="280"/>
+ <dimensions width="240" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_oxaloacetate_cyt" species="oxaloacetate_cyt">
+ <boundingBox id="bb_sg_oxaloacetate_cyt">
+ <position x="580" y="480"/>
+ <dimensions width="240" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_aspartate_cyt" species="aspartate_cyt">
+ <boundingBox id="bb_sg_aspartate_cyt">
+ <position x="580" y="680"/>
+ <dimensions width="240" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_glutamate_cyt" species="glutamate_cyt">
+ <boundingBox id="bb_sg_glutamate_cyt">
+ <position x="800" y="610"/>
+ <dimensions width="240" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_aKetoglutarate_cyt" species="aKetoglutarate_cyt">
+ <boundingBox id="bb_sg_aKetoglutarate_cyt">
+ <position x="860" y="500"/>
+ <dimensions width="280" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_nad_cyt" species="nad_cyt">
+ <boundingBox id="bb_sg_nad_cyt">
+ <position x="520" y="350"/>
+ <dimensions width="100" height="24"/>
+ </boundingBox>
+ </speciesGlyph>
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+ </boundingBox>
+ </speciesGlyph>
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+ <speciesGlyph id="SpeciesGlyph_oxaloacetate_mito3" species="oxaloacetate_mito3">
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+ </boundingBox>
+ </speciesGlyph>
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+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_aKetoglutarate_mito3" species="aKetoglutarate_mito3">
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+ </boundingBox>
+ </speciesGlyph>
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+ </speciesGlyph>
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+ </speciesGlyph>
+ </listOfSpeciesGlyphs>
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+ </listOfCurveSegments>
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+ </speciesReferenceGlyph>
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+ </speciesReferenceGlyph>
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+ </speciesReferenceGlyph>
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+ </speciesReferenceGlyph>
+ </listOfSpeciesReferenceGlyphs>
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+ <reactionGlyph id="rg_aspartateat_cyt" reaction="reaction_aspartateat_cyt">
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+ </listOfCurveSegments>
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+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_glutamate_cyt_1" speciesReference="sr_glutamate_cyt_1" speciesGlyph="SpeciesGlyph_glutamate_cyt" role="substrate">
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+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_aspartate_cyt_1" speciesReference="sr_aspartate_cyt_1" speciesGlyph="SpeciesGlyph_aspartate_cyt" role="product">
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+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_aKetoglutaratecyt_1" speciesReference="sr_aKetoglutarate_cyt_1" speciesGlyph="SpeciesGlyph_aKetoglutarate_cyt" role="product">
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+ <curveSegment xsi:type="CubicBezier">
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+ </speciesReferenceGlyph>
+ </listOfSpeciesReferenceGlyphs>
+ </reactionGlyph>
+ <reactionGlyph id="rg_malatedh_mito3" reaction="reaction_malatedh_mito3">
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+ </speciesReferenceGlyph>
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+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
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+ </speciesReferenceGlyph>
+ </listOfSpeciesReferenceGlyphs>
+ </reactionGlyph> -->
+ </listOfReactionGlyphs>
+ <listOfTextGlyphs>
+ <textGlyph id="TextGlyph_Hepatocyte" graphicalObject="CompartmentGlyph_1" originOfText="Hepatocyte">
+ <boundingBox id="bb_tg_compartment">
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+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_oxaloacetate_mito3" graphicalObject="SpeciesGlyph_oxaloacetate_mito3" originOfText="oxaloacetate_mito3">
+ <boundingBox id="bb_tg_oxaloacetate_mito3">
+ <position x="1860" y="280"/>
+ <dimensions width="220" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_aspartate_mito3" graphicalObject="SpeciesGlyph_aspartate_mito3" originOfText="aspartate_mito3">
+ <boundingBox id="bb_tg_aspartate_mito3">
+ <position x="1860" y="480"/>
+ <dimensions width="220" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_glutamate_mito3" graphicalObject="SpeciesGlyph_glutamate_mito3" originOfText="glutamate_mito3">
+ <boundingBox id="bb_tg_glutamate_mito3">
+ <position x="1560" y="430"/>
+ <dimensions width="220" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_aKetoglutarate_mito3" graphicalObject="SpeciesGlyph_aKetoglutarate_mito3" originOfText="aKetoglutarate_mito3">
+ <boundingBox id="bb_tg_aKetoglutarate_mito3">
+ <position x="1540" y="300"/>
+ <dimensions width="260" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_nad_mito3" graphicalObject="SpeciesGlyph_nad_mito3" originOfText="nad_mito3">
+ <boundingBox id="bb_tg_nad_mito3">
+ <position x="2055" y="150"/>
+ <dimensions width="80" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_nadh_mito3" graphicalObject="SpeciesGlyph_nadh_mito3" originOfText="nadh_mito3">
+ <boundingBox id="bb_tg_nadh_mito3">
+ <position x="2055" y="230"/>
+ <dimensions width="80" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_h_mito3" graphicalObject="SpeciesGlyph_h_mito3" originOfText="h_mito3">
+ <boundingBox id="bb_tg_h_mito3">
+ <position x="2205" y="230"/>
+ <dimensions width="30" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="tg_rg_malatedh_mito3" graphicalObject="rg_malatedh_mito3" originOfText="reaction_malatedh_mito3">
+ <boundingBox id="bb_tg_rg_malatedh_mito3">
+ <position x="1740" y="185"/>
+ <dimensions width="220" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="tg_rg_aspartateat_mito3" graphicalObject="rg_aspartateat_mito3" originOfText="reaction_aspartateat_mito3">
+ <boundingBox id="bb_tg_rg_aspartateat_mito3">
+ <position x="1970" y="385"/>
+ <dimensions width="260" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="tg_rg_aspartateCarrier" graphicalObject="rg_aspartateCarrier" originOfText="aspartateCarrier">
+ <boundingBox id="bb_tg_rg_aspartateCarrier">
+ <position x="1380" y="500"/>
+ <dimensions width="160" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="tg_rg_malateCarrier" graphicalObject="rg_malateCarrier" originOfText="malateCarrier">
+ <boundingBox id="bb_tg_rg_malateCarrier">
+ <position x="1360" y="330"/>
+ <dimensions width="140" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ </listOfTextGlyphs>
+ </layout>
+ </listOfLayouts>
+ </annotation>
+ <listOfCompartments>
+ <compartment id="Hepatocyte" name="Hepatocyte" size="1"/>
+ <compartment id="Mito_1" name="Mito 1" size="1" outside="Hepatocyte"/>
+ <compartment id="Mito_2" name="Mito 2" size="1" outside="Hepatocyte"/>
+ <compartment id="Mito_3" name="Mito 3" size="1" outside="Hepatocyte"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="malate_cyt" name="Malate" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="malate_mito1" name="Malate" compartment="Mito_1" initialConcentration="0"/>
+ <species id="malate_mito2" name="Malate" compartment="Mito_2" initialConcentration="0"/>
+ <species id="malate_mito3" name="Malate" compartment="Mito_3" initialConcentration="0"/>
+ <species id="oxaloacetate_cyt" name="Oxaloacetate" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="oxaloacetate_mito1" name="Oxaloacetate" compartment="Mito_1" initialConcentration="0"/>
+ <species id="oxaloacetate_mito2" name="Oxaloacetate" compartment="Mito_2" initialConcentration="0"/>
+ <species id="oxaloacetate_mito3" name="Oxaloacetate" compartment="Mito_3" initialConcentration="0"/>
+ <species id="aspartate_cyt" name="Aspartate" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="aspartate_mito1" name="Aspartate" compartment="Mito_1" initialConcentration="0"/>
+ <species id="aspartate_mito2" name="Aspartate" compartment="Mito_2" initialConcentration="0"/>
+ <species id="aspartate_mito3" name="Aspartate" compartment="Mito_3" initialConcentration="0"/>
+ <species id="glutamate_cyt" name="Glutamate" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="glutamate_mito1" name="Glutamate" compartment="Mito_1" initialConcentration="0"/>
+ <species id="glutamate_mito2" name="Glutamate" compartment="Mito_2" initialConcentration="0"/>
+ <species id="glutamate_mito3" name="Glutamate" compartment="Mito_3" initialConcentration="0"/>
+ <species id="aKetoglutarate_cyt" name="alpha-Ketoglutarate" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="aKetoglutarate_mito1" name="alpha-Ketoglutarate" compartment="Mito_1" initialConcentration="0"/>
+ <species id="aKetoglutarate_mito2" name="alpha-Ketoglutarate" compartment="Mito_2" initialConcentration="0"/>
+ <species id="aKetoglutarate_mito3" name="alpha-Ketoglutarate" compartment="Mito_3" initialConcentration="0"/>
+ <species id="h_cyt" name="H+" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="h_mito1" name="H+" compartment="Mito_1" initialConcentration="0"/>
+ <species id="h_mito2" name="H+" compartment="Mito_2" initialConcentration="0"/>
+ <species id="h_mito3" name="H+" compartment="Mito_3" initialConcentration="0"/>
+ <species id="nad_cyt" name="NAD+" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="nad_mito1" name="NAD+" compartment="Mito_1" initialConcentration="0"/>
+ <species id="nad_mito2" name="NAD+" compartment="Mito_2" initialConcentration="0"/>
+ <species id="nad_mito3" name="NAD+" compartment="Mito_3" initialConcentration="0"/>
+ <species id="nadh_cyt" name="NADH" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="nadh_mito1" name="NADH" compartment="Mito_1" initialConcentration="0"/>
+ <species id="nadh_mito2" name="NADH" compartment="Mito_2" initialConcentration="0"/>
+ <species id="nadh_mito3" name="NADH" compartment="Mito_3" initialConcentration="0"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="reaction_malatedh_cyt" name="malate dehydrogenase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="malate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_malate_cyt"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="nad_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nad_cyt"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="nadh_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nadh_cyt"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="h_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_h_cyt"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="oxaloacetate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_cyt_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="reaction_aspartateat_cyt" name="aspartate aminotransferase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="oxaloacetate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_cyt_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="glutamate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_glutamate_cyt_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="aspartate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aspartate_cyt_1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="aKetoglutarate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aKetoglutarate_cyt_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="reaction_malatedh_mito1" name="malate dehydrogenase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="malate_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_malate_mito1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="nad_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nad_mito1"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="nadh_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nadh_mito1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="h_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_h_mito1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="oxaloacetate_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_mito1_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="reaction_aspartateat_mito1" name="aspartate aminotransferase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="oxaloacetate_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_mito1_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="glutamate_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_glutamate_mito1"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="aspartate_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aspartate_mito1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="aKetoglutarate_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aKetoglutarate_mito1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="reaction_malatedh_mito2" name="malate dehydrogenase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="malate_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_malate_mito2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="nad_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nad_mito2"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="nadh_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nadh_mito2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="h_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_h_mito2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="oxaloacetate_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_mito2_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="reaction_aspartateat_mito2" name="aspartate aminotransferase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="oxaloacetate_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_mito2_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="glutamate_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_glutamate_mito2"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="aspartate_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aspartate_mito2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="aKetoglutarate_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aKetoglutarate_mito2"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="reaction_malatedh_mito3" name="malate dehydrogenase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="malate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_malate_mito3"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="nad_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nad_mito3"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="nadh_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nadh_mito3"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="h_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_h_mito3"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="oxaloacetate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_mito3_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="reaction_aspartateat_mito3" name="aspartate aminotransferase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="oxaloacetate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_mito3_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="glutamate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_glutamate_mito3_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="aspartate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aspartate_mito3_1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="aKetoglutarate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aKetoglutarate_mito3_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="aspartateCarrier" name="aspartate carrier">
+ <listOfReactants>
+ <speciesReference species="glutamate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_glutamate_mito3_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="aspartate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aspartate_cyt_2"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="glutamate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_glutamate_cyt_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="aspartate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aspartate_mito3_2"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="malateCarrier" name="malate carrier">
+ <listOfReactants>
+ <speciesReference species="aKetoglutarate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aKetoglutarate_mito3_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="malate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_malate_cyt_2"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="aKetoglutarate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aKetoglutarate_cyt_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="malate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_malate_mito3_2"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/converter-sbml/testFiles/layoutExample/example4_level3.xml b/converter-sbml/testFiles/layoutExample/example4_level3.xml
new file mode 100644
index 0000000000000000000000000000000000000000..f6d6990b0b12578b5f748e512235e1ac29ae54cb
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/example4_level3.xml
@@ -0,0 +1,845 @@
+<?xml version='1.0' encoding='utf-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" layout:required="false" level="3" version="1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+ <model areaUnits="area" extentUnits="substance" id="TestModel" lengthUnits="metre" substanceUnits="substance" timeUnits="second" volumeUnits="volume">
+ <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <layout:layout layout:id="Layout_1">
+ <layout:dimensions layout:height="1000" layout:width="2300" />
+ <layout:listOfCompartmentGlyphs>
+ <layout:compartmentGlyph layout:compartment="Hepatocyte" layout:id="CompartmentGlyph_1">
+ <layout:boundingBox layout:id="bb_compartment">
+ <layout:position layout:x="10" layout:y="10" />
+ <layout:dimensions layout:height="980" layout:width="1380" />
+ </layout:boundingBox>
+ </layout:compartmentGlyph>
+ <layout:compartmentGlyph layout:compartment="Mito_1" layout:id="Mito1_Glyph">
+ <layout:boundingBox layout:id="bb_mito1">
+ <layout:position layout:x="100" layout:y="100" />
+ <layout:dimensions layout:height="100" layout:width="300" />
+ </layout:boundingBox>
+ </layout:compartmentGlyph>
+ <layout:compartmentGlyph layout:compartment="Mito_2" layout:id="Mito2_Glyph">
+ <layout:boundingBox layout:id="bb_mito2">
+ <layout:position layout:x="200" layout:y="650" />
+ <layout:dimensions layout:height="100" layout:width="300" />
+ </layout:boundingBox>
+ </layout:compartmentGlyph>
+ <layout:compartmentGlyph layout:compartment="Mito_3" layout:id="Mito3_Glyph">
+ <layout:boundingBox layout:id="bb_mito3">
+ <layout:position layout:x="1000" layout:y="800" />
+ <layout:dimensions layout:height="100" layout:width="300" />
+ </layout:boundingBox>
+ </layout:compartmentGlyph>
+ </layout:listOfCompartmentGlyphs>
+ <layout:listOfSpeciesGlyphs>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_malate_cyt" layout:species="malate_cyt">
+ <layout:boundingBox layout:id="bb_sg_malate_cyt">
+ <layout:position layout:x="580" layout:y="280" />
+ <layout:dimensions layout:height="36" layout:width="240" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_oxaloacetate_cyt" layout:species="oxaloacetate_cyt">
+ <layout:boundingBox layout:id="bb_sg_oxaloacetate_cyt">
+ <layout:position layout:x="580" layout:y="480" />
+ <layout:dimensions layout:height="36" layout:width="240" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_aspartate_cyt" layout:species="aspartate_cyt">
+ <layout:boundingBox layout:id="bb_sg_aspartate_cyt">
+ <layout:position layout:x="580" layout:y="680" />
+ <layout:dimensions layout:height="36" layout:width="240" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_glutamate_cyt" layout:species="glutamate_cyt">
+ <layout:boundingBox layout:id="bb_sg_glutamate_cyt">
+ <layout:position layout:x="800" layout:y="610" />
+ <layout:dimensions layout:height="36" layout:width="240" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_aKetoglutarate_cyt" layout:species="aKetoglutarate_cyt">
+ <layout:boundingBox layout:id="bb_sg_aKetoglutarate_cyt">
+ <layout:position layout:x="860" layout:y="500" />
+ <layout:dimensions layout:height="36" layout:width="280" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_nad_cyt" layout:species="nad_cyt">
+ <layout:boundingBox layout:id="bb_sg_nad_cyt">
+ <layout:position layout:x="520" layout:y="350" />
+ <layout:dimensions layout:height="24" layout:width="100" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_nadh_cyt" layout:species="nadh_cyt">
+ <layout:boundingBox layout:id="bb_sg_nadh_cyt">
+ <layout:position layout:x="520" layout:y="430" />
+ <layout:dimensions layout:height="24" layout:width="100" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_h_cyt" layout:species="h_cyt">
+ <layout:boundingBox layout:id="bb_sg_h_cyt">
+ <layout:position layout:x="430" layout:y="430" />
+ <layout:dimensions layout:height="24" layout:width="40" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
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+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_malate_cyt" layout:id="TextGlyph_malate_cyt" layout:originOfText="malate_cyt">
+ <layout:boundingBox layout:id="bb_tg_malatate_cyt">
+ <layout:position layout:x="590" layout:y="280" />
+ <layout:dimensions layout:height="36" layout:width="220" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_oxaloacetate_cyt" layout:id="TextGlyph_oxaloacetate_cyt" layout:originOfText="oxaloacetate_cyt">
+ <layout:boundingBox layout:id="bb_tg_oxaloacetate_cyt">
+ <layout:position layout:x="590" layout:y="480" />
+ <layout:dimensions layout:height="36" layout:width="220" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_aspartate_cyt" layout:id="TextGlyph_aspartate_cyt" layout:originOfText="aspartate_cyt">
+ <layout:boundingBox layout:id="bb_tg_aspartate_cyt">
+ <layout:position layout:x="590" layout:y="680" />
+ <layout:dimensions layout:height="36" layout:width="220" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_glutamate_cyt" layout:id="TextGlyph_glutamate_cyt" layout:originOfText="glutamate_cyt">
+ <layout:boundingBox layout:id="bb_tg_glutamate_cyt">
+ <layout:position layout:x="810" layout:y="610" />
+ <layout:dimensions layout:height="36" layout:width="220" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_aKetoglutarate_cyt" layout:id="TextGlyph_aKetoglutarate_cyt" layout:originOfText="aKetoglutarate_cyt">
+ <layout:boundingBox layout:id="bb_tg_aKetoglutarate_cyt">
+ <layout:position layout:x="870" layout:y="500" />
+ <layout:dimensions layout:height="36" layout:width="260" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_nad_cyt" layout:id="TextGlyph_nad_cyt" layout:originOfText="nad_cyt">
+ <layout:boundingBox layout:id="bb_tg_nad_cyt">
+ <layout:position layout:x="525" layout:y="350" />
+ <layout:dimensions layout:height="24" layout:width="80" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_nadh_cyt" layout:id="TextGlyph_nadh_cyt" layout:originOfText="nadh_cyt">
+ <layout:boundingBox layout:id="bb_tg_nadh_cyt">
+ <layout:position layout:x="525" layout:y="430" />
+ <layout:dimensions layout:height="24" layout:width="80" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_h_cyt" layout:id="TextGlyph_h_cyt" layout:originOfText="h_cyt">
+ <layout:boundingBox layout:id="bb_tg_h_cyt">
+ <layout:position layout:x="435" layout:y="430" />
+ <layout:dimensions layout:height="24" layout:width="30" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="rg_malatedh_cyt" layout:id="tg_rg_malaltedh_cyt" layout:originOfText="reaction_malatedh_cyt">
+ <layout:boundingBox layout:id="bb_tg_rg_malaltedh_cyt">
+ <layout:position layout:x="700" layout:y="385" />
+ <layout:dimensions layout:height="24" layout:width="210" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="rg_aspartateat_cyt" layout:id="tg_rg_aspartateat_cyt" layout:originOfText="reaction_aspartateat_cyt">
+ <layout:boundingBox layout:id="bb_tg_rg_aspartateat_cyt">
+ <layout:position layout:x="440" layout:y="585" />
+ <layout:dimensions layout:height="24" layout:width="260" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_malate_mito3" layout:id="TextGlyph_malate_mito3" layout:originOfText="malate_mito3">
+ <layout:boundingBox layout:id="bb_tg_malatate_mito3">
+ <layout:position layout:x="1860" layout:y="80" />
+ <layout:dimensions layout:height="36" layout:width="220" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_oxaloacetate_mito3" layout:id="TextGlyph_oxaloacetate_mito3" layout:originOfText="oxaloacetate_mito3">
+ <layout:boundingBox layout:id="bb_tg_oxaloacetate_mito3">
+ <layout:position layout:x="1860" layout:y="280" />
+ <layout:dimensions layout:height="36" layout:width="220" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_aspartate_mito3" layout:id="TextGlyph_aspartate_mito3" layout:originOfText="aspartate_mito3">
+ <layout:boundingBox layout:id="bb_tg_aspartate_mito3">
+ <layout:position layout:x="1860" layout:y="480" />
+ <layout:dimensions layout:height="36" layout:width="220" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_glutamate_mito3" layout:id="TextGlyph_glutamate_mito3" layout:originOfText="glutamate_mito3">
+ <layout:boundingBox layout:id="bb_tg_glutamate_mito3">
+ <layout:position layout:x="1560" layout:y="430" />
+ <layout:dimensions layout:height="36" layout:width="220" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_aKetoglutarate_mito3" layout:id="TextGlyph_aKetoglutarate_mito3" layout:originOfText="aKetoglutarate_mito3">
+ <layout:boundingBox layout:id="bb_tg_aKetoglutarate_mito3">
+ <layout:position layout:x="1540" layout:y="300" />
+ <layout:dimensions layout:height="36" layout:width="260" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_nad_mito3" layout:id="TextGlyph_nad_mito3" layout:originOfText="nad_mito3">
+ <layout:boundingBox layout:id="bb_tg_nad_mito3">
+ <layout:position layout:x="2055" layout:y="150" />
+ <layout:dimensions layout:height="24" layout:width="80" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_nadh_mito3" layout:id="TextGlyph_nadh_mito3" layout:originOfText="nadh_mito3">
+ <layout:boundingBox layout:id="bb_tg_nadh_mito3">
+ <layout:position layout:x="2055" layout:y="230" />
+ <layout:dimensions layout:height="24" layout:width="80" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="SpeciesGlyph_h_mito3" layout:id="TextGlyph_h_mito3" layout:originOfText="h_mito3">
+ <layout:boundingBox layout:id="bb_tg_h_mito3">
+ <layout:position layout:x="2205" layout:y="230" />
+ <layout:dimensions layout:height="24" layout:width="30" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="rg_malatedh_mito3" layout:id="tg_rg_malatedh_mito3" layout:originOfText="reaction_malatedh_mito3">
+ <layout:boundingBox layout:id="bb_tg_rg_malatedh_mito3">
+ <layout:position layout:x="1740" layout:y="185" />
+ <layout:dimensions layout:height="24" layout:width="220" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="rg_aspartateat_mito3" layout:id="tg_rg_aspartateat_mito3" layout:originOfText="reaction_aspartateat_mito3">
+ <layout:boundingBox layout:id="bb_tg_rg_aspartateat_mito3">
+ <layout:position layout:x="1970" layout:y="385" />
+ <layout:dimensions layout:height="24" layout:width="260" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="rg_aspartateCarrier" layout:id="tg_rg_aspartateCarrier" layout:originOfText="aspartateCarrier">
+ <layout:boundingBox layout:id="bb_tg_rg_aspartateCarrier">
+ <layout:position layout:x="1380" layout:y="500" />
+ <layout:dimensions layout:height="24" layout:width="160" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="rg_malateCarrier" layout:id="tg_rg_malateCarrier" layout:originOfText="malateCarrier">
+ <layout:boundingBox layout:id="bb_tg_rg_malateCarrier">
+ <layout:position layout:x="1360" layout:y="330" />
+ <layout:dimensions layout:height="24" layout:width="140" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ </layout:listOfTextGlyphs>
+ </layout:layout>
+ </layout:listOfLayouts>
+ <listOfUnitDefinitions>
+ <unitDefinition id="volume">
+ <listOfUnits>
+ <unit exponent="1" kind="litre" multiplier="1" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="substance">
+ <listOfUnits>
+ <unit exponent="1" kind="mole" multiplier="1" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="area">
+ <listOfUnits>
+ <unit exponent="2" kind="metre" multiplier="1" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment constant="true" id="Hepatocyte" name="Hepatocyte" size="1" spatialDimensions="3" units="volume" />
+ <compartment constant="true" id="Mito_1" name="Mito 1" size="1" spatialDimensions="3" units="volume" />
+ <compartment constant="true" id="Mito_2" name="Mito 2" size="1" spatialDimensions="3" units="volume" />
+ <compartment constant="true" id="Mito_3" name="Mito 3" size="1" spatialDimensions="3" units="volume" />
+ </listOfCompartments>
+ <listOfSpecies>
+ <species boundaryCondition="false" compartment="Hepatocyte" constant="false" hasOnlySubstanceUnits="false" id="malate_cyt" initialConcentration="0" name="Malate" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_1" constant="false" hasOnlySubstanceUnits="false" id="malate_mito1" initialConcentration="0" name="Malate" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_2" constant="false" hasOnlySubstanceUnits="false" id="malate_mito2" initialConcentration="0" name="Malate" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_3" constant="false" hasOnlySubstanceUnits="false" id="malate_mito3" initialConcentration="0" name="Malate" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Hepatocyte" constant="false" hasOnlySubstanceUnits="false" id="oxaloacetate_cyt" initialConcentration="0" name="Oxaloacetate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_1" constant="false" hasOnlySubstanceUnits="false" id="oxaloacetate_mito1" initialConcentration="0" name="Oxaloacetate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_2" constant="false" hasOnlySubstanceUnits="false" id="oxaloacetate_mito2" initialConcentration="0" name="Oxaloacetate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_3" constant="false" hasOnlySubstanceUnits="false" id="oxaloacetate_mito3" initialConcentration="0" name="Oxaloacetate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Hepatocyte" constant="false" hasOnlySubstanceUnits="false" id="aspartate_cyt" initialConcentration="0" name="Aspartate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_1" constant="false" hasOnlySubstanceUnits="false" id="aspartate_mito1" initialConcentration="0" name="Aspartate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_2" constant="false" hasOnlySubstanceUnits="false" id="aspartate_mito2" initialConcentration="0" name="Aspartate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_3" constant="false" hasOnlySubstanceUnits="false" id="aspartate_mito3" initialConcentration="0" name="Aspartate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Hepatocyte" constant="false" hasOnlySubstanceUnits="false" id="glutamate_cyt" initialConcentration="0" name="Glutamate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_1" constant="false" hasOnlySubstanceUnits="false" id="glutamate_mito1" initialConcentration="0" name="Glutamate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_2" constant="false" hasOnlySubstanceUnits="false" id="glutamate_mito2" initialConcentration="0" name="Glutamate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_3" constant="false" hasOnlySubstanceUnits="false" id="glutamate_mito3" initialConcentration="0" name="Glutamate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Hepatocyte" constant="false" hasOnlySubstanceUnits="false" id="aKetoglutarate_cyt" initialConcentration="0" name="alpha-Ketoglutarate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_1" constant="false" hasOnlySubstanceUnits="false" id="aKetoglutarate_mito1" initialConcentration="0" name="alpha-Ketoglutarate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_2" constant="false" hasOnlySubstanceUnits="false" id="aKetoglutarate_mito2" initialConcentration="0" name="alpha-Ketoglutarate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_3" constant="false" hasOnlySubstanceUnits="false" id="aKetoglutarate_mito3" initialConcentration="0" name="alpha-Ketoglutarate"
+ substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Hepatocyte" constant="false" hasOnlySubstanceUnits="false" id="h_cyt" initialConcentration="0" name="H+" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_1" constant="false" hasOnlySubstanceUnits="false" id="h_mito1" initialConcentration="0" name="H+" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_2" constant="false" hasOnlySubstanceUnits="false" id="h_mito2" initialConcentration="0" name="H+" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_3" constant="false" hasOnlySubstanceUnits="false" id="h_mito3" initialConcentration="0" name="H+" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Hepatocyte" constant="false" hasOnlySubstanceUnits="false" id="nad_cyt" initialConcentration="0" name="NAD+" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_1" constant="false" hasOnlySubstanceUnits="false" id="nad_mito1" initialConcentration="0" name="NAD+" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_2" constant="false" hasOnlySubstanceUnits="false" id="nad_mito2" initialConcentration="0" name="NAD+" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_3" constant="false" hasOnlySubstanceUnits="false" id="nad_mito3" initialConcentration="0" name="NAD+" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Hepatocyte" constant="false" hasOnlySubstanceUnits="false" id="nadh_cyt" initialConcentration="0" name="NADH" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_1" constant="false" hasOnlySubstanceUnits="false" id="nadh_mito1" initialConcentration="0" name="NADH" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_2" constant="false" hasOnlySubstanceUnits="false" id="nadh_mito2" initialConcentration="0" name="NADH" substanceUnits="substance" />
+ <species boundaryCondition="false" compartment="Mito_3" constant="false" hasOnlySubstanceUnits="false" id="nadh_mito3" initialConcentration="0" name="NADH" substanceUnits="substance" />
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction fast="false" id="reaction_malatedh_cyt" name="malate dehydrogenase" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="sr_malate_cyt" species="malate_cyt" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_nad_cyt" species="nad_cyt" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="sr_nadh_cyt" species="nadh_cyt" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_h_cyt" species="h_cyt" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_oxaloacetate_cyt_1" species="oxaloacetate_cyt" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="reaction_aspartateat_cyt" name="aspartate aminotransferase" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="sr_oxaloacetate_cyt_2" species="oxaloacetate_cyt" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_glutamate_cyt_1" species="glutamate_cyt" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="sr_aspartate_cyt_1" species="aspartate_cyt" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_aKetoglutarate_cyt_1" species="aKetoglutarate_cyt" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="reaction_malatedh_mito1" name="malate dehydrogenase" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="sr_malate_mito1" species="malate_mito1" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_nad_mito1" species="nad_mito1" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="sr_nadh_mito1" species="nadh_mito1" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_h_mito1" species="h_mito1" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_oxaloacetate_mito1_1" species="oxaloacetate_mito1" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="reaction_aspartateat_mito1" name="aspartate aminotransferase" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="sr_oxaloacetate_mito1_2" species="oxaloacetate_mito1" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_glutamate_mito1" species="glutamate_mito1" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="sr_aspartate_mito1" species="aspartate_mito1" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_aKetoglutarate_mito1" species="aKetoglutarate_mito1" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="reaction_malatedh_mito2" name="malate dehydrogenase" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="sr_malate_mito2" species="malate_mito2" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_nad_mito2" species="nad_mito2" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="sr_nadh_mito2" species="nadh_mito2" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_h_mito2" species="h_mito2" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_oxaloacetate_mito2_1" species="oxaloacetate_mito2" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="reaction_aspartateat_mito2" name="aspartate aminotransferase" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="sr_oxaloacetate_mito2_2" species="oxaloacetate_mito2" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_glutamate_mito2" species="glutamate_mito2" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="sr_aspartate_mito2" species="aspartate_mito2" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_aKetoglutarate_mito2" species="aKetoglutarate_mito2" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="reaction_malatedh_mito3" name="malate dehydrogenase" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="sr_malate_mito3" species="malate_mito3" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_nad_mito3" species="nad_mito3" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="sr_nadh_mito3" species="nadh_mito3" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_h_mito3" species="h_mito3" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_oxaloacetate_mito3_1" species="oxaloacetate_mito3" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="reaction_aspartateat_mito3" name="aspartate aminotransferase" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="sr_oxaloacetate_mito3_2" species="oxaloacetate_mito3" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_glutamate_mito3_1" species="glutamate_mito3" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="sr_aspartate_mito3_1" species="aspartate_mito3" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_aKetoglutarate_mito3_1" species="aKetoglutarate_mito3" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="aspartateCarrier" name="aspartate carrier" reversible="true">
+ <listOfReactants>
+ <speciesReference constant="true" id="sr_glutamate_mito3_2" species="glutamate_mito3" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_aspartate_cyt_2" species="aspartate_cyt" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="sr_glutamate_cyt_2" species="glutamate_cyt" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_aspartate_mito3_2" species="aspartate_mito3" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="malateCarrier" name="malate carrier" reversible="true">
+ <listOfReactants>
+ <speciesReference constant="true" id="sr_aKetoglutarate_mito3_2" species="aKetoglutarate_mito3" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_malate_cyt_2" species="malate_cyt" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="sr_aKetoglutarate_cyt_2" species="aKetoglutarate_cyt" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_malate_mito3_2" species="malate_mito3" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/converter-sbml/testFiles/layoutExample/example5.xml b/converter-sbml/testFiles/layoutExample/example5.xml
new file mode 100644
index 0000000000000000000000000000000000000000..0be6a6e8ec40b6dcebe363b08f75ff7cf8a1d7f2
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/example5.xml
@@ -0,0 +1,1020 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+ <model id="TestModel">
+ <annotation>
+ <listOfLayouts xmlns="http://projects.eml.org/bcb/sbml/level2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <layout id="Layout_1">
+ <dimensions width="2300" height="1000"/>
+ <listOfCompartmentGlyphs>
+ <compartmentGlyph id="CompartmentGlyph_1" compartment="Hepatocyte">
+ <boundingBox id="bb_compartment">
+ <position x="10" y="10"/>
+ <dimensions width="1380" height="980"/>
+ </boundingBox>
+ </compartmentGlyph>
+ <compartmentGlyph id="Mito1_Glyph" compartment="Mito_1">
+ <boundingBox id="bb_mito1">
+ <position x="100" y="100"/>
+ <dimensions width="300" height="100"/>
+ </boundingBox>
+ </compartmentGlyph>
+ <compartmentGlyph id="Mito2_Glyph" compartment="Mito_2">
+ <boundingBox id="bb_mito2">
+ <position x="200" y="650"/>
+ <dimensions width="300" height="100"/>
+ </boundingBox>
+ </compartmentGlyph>
+ <compartmentGlyph id="Mito3_Glyph" compartment="Mito_3">
+ <boundingBox id="bb_mito3">
+ <position x="1000" y="800"/>
+ <dimensions width="300" height="100"/>
+ </boundingBox>
+ </compartmentGlyph>
+ <compartmentGlyph id="Mito3_Glyph_2" compartment="Mito_3">
+ <boundingBox id="bb_mito3_2">
+ <position x="1470" y="30"/>
+ <dimensions width="820" height="536"/>
+ </boundingBox>
+ </compartmentGlyph>
+ </listOfCompartmentGlyphs>
+ <listOfSpeciesGlyphs>
+ <speciesGlyph id="SpeciesGlyph_malate_cyt" species="malate_cyt">
+ <boundingBox id="bb_sg_malate_cyt">
+ <position x="580" y="280"/>
+ <dimensions width="240" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_oxaloacetate_cyt" species="oxaloacetate_cyt">
+ <boundingBox id="bb_sg_oxaloacetate_cyt">
+ <position x="580" y="480"/>
+ <dimensions width="240" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_aspartate_cyt" species="aspartate_cyt">
+ <boundingBox id="bb_sg_aspartate_cyt">
+ <position x="580" y="680"/>
+ <dimensions width="240" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_glutamate_cyt" species="glutamate_cyt">
+ <boundingBox id="bb_sg_glutamate_cyt">
+ <position x="800" y="610"/>
+ <dimensions width="240" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_aKetoglutarate_cyt" species="aKetoglutarate_cyt">
+ <boundingBox id="bb_sg_aKetoglutarate_cyt">
+ <position x="860" y="500"/>
+ <dimensions width="280" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_nad_cyt" species="nad_cyt">
+ <boundingBox id="bb_sg_nad_cyt">
+ <position x="520" y="350"/>
+ <dimensions width="100" height="24"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_nadh_cyt" species="nadh_cyt">
+ <boundingBox id="bb_sg_nadh_cyt">
+ <position x="520" y="430"/>
+ <dimensions width="100" height="24"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_h_cyt" species="h_cyt">
+ <boundingBox id="bb_sg_h_cyt">
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+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_malate_mito3" species="malate_mito3">
+ <boundingBox id="bb_sg_malate_mito3">
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+ <dimensions width="240" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_oxaloacetate_mito3" species="oxaloacetate_mito3">
+ <boundingBox id="bb_sg_oxaloacetate_mito3">
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+ <dimensions width="240" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_aspartate_mito3" species="aspartate_mito3">
+ <boundingBox id="bb_sg_aspartate_mito3">
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+ <dimensions width="240" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_glutamate_mito3" species="glutamate_mito3">
+ <boundingBox id="bb_sg_glutamate_mito3">
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+ <dimensions width="240" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_aKetoglutarate_mito3" species="aKetoglutarate_mito3">
+ <boundingBox id="bb_sg_aKetoglutarate_mito3">
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+ <dimensions width="280" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_nad_mito3" species="nad_mito3">
+ <boundingBox id="bb_sg_nad_mito3">
+ <position x="2050" y="150"/>
+ <dimensions width="100" height="24"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_nadh_mito3" species="nadh_mito3">
+ <boundingBox id="bb_sg_nadh_mito3">
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+ <dimensions width="100" height="24"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_h_mito3" species="h_mito3">
+ <boundingBox id="bb_sg_h_mito3">
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+ <dimensions width="40" height="24"/>
+ </boundingBox>
+ </speciesGlyph>
+ </listOfSpeciesGlyphs>
+ <listOfReactionGlyphs>
+ <reactionGlyph id="rg_malatedh_cyt" reaction="reaction_malatedh_cyt">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
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+ <end x="700" y="415"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ <listOfSpeciesReferenceGlyphs>
+ <speciesReferenceGlyph id="srg_malate_cyt_1" speciesReference="sr_malate_cyt" speciesGlyph="SpeciesGlyph_malate_cyt" role="substrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
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+ <end x="700" y="316"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_nad_cyt" speciesReference="sr_nad_cyt" speciesGlyph="SpeciesGlyph_nad_cyt" role="substrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
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+ <end x="620" y="362"/>
+ <basePoint1 x="700" y="362"/>
+ <basePoint2 x="700" y="362"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_oxaloacetate_cyt_1" speciesReference="sr_oxaloacetate_cyt_1" speciesGlyph="SpeciesGlyph_oxaloacetate_cyt" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
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+ <end x="700" y="480"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_nadh_cyt" speciesReference="sr_nadh_cyt" speciesGlyph="SpeciesGlyph_nadh_cyt" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
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+ <end x="620" y="442"/>
+ <basePoint1 x="700" y="442"/>
+ <basePoint2 x="700" y="442"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_h_cyt" speciesReference="sr_h_cyt" speciesGlyph="SpeciesGlyph_h_cyt" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
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+ <end x="470" y="430"/>
+ <basePoint1 x="570" y="415"/>
+ <basePoint2 x="570" y="415"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ </listOfSpeciesReferenceGlyphs>
+ </reactionGlyph>
+ <reactionGlyph id="rg_aspartateat_cyt" reaction="reaction_aspartateat_cyt">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
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+ <end x="700" y="615"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ <listOfSpeciesReferenceGlyphs>
+ <speciesReferenceGlyph id="srg_oxaloacetate_cyt_2" speciesReference="sr_oxaloacetate_cyt_2" speciesGlyph="SpeciesGlyph_oxaloacetate_cyt" role="substrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
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+ <end x="700" y="516"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_glutamate_cyt_1" speciesReference="sr_glutamate_cyt_1" speciesGlyph="SpeciesGlyph_glutamate_cyt" role="substrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
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+ <end x="800" y="628"/>
+ <basePoint1 x="750" y="581"/>
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+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_aspartate_cyt_1" speciesReference="sr_aspartate_cyt_1" speciesGlyph="SpeciesGlyph_aspartate_cyt" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
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+ <end x="700" y="680"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_aKetoglutaratecyt_1" speciesReference="sr_aKetoglutarate_cyt_1" speciesGlyph="SpeciesGlyph_aKetoglutarate_cyt" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
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+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ </listOfSpeciesReferenceGlyphs>
+ </reactionGlyph>
+ <reactionGlyph id="rg_malatedh_mito3" reaction="reaction_malatedh_mito3">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
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+ <end x="1970" y="215"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ <listOfSpeciesReferenceGlyphs>
+ <speciesReferenceGlyph id="srg_malate_mito3_1" speciesReference="sr_malate_mito3" speciesGlyph="SpeciesGlyph_malate_mito3" role="substrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
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+ <end x="1970" y="116"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_nad_mito3" speciesReference="sr_nad_mito3" speciesGlyph="SpeciesGlyph_nad_mito3" role="substrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
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+ <basePoint1 x="1970" y="162"/>
+ <basePoint2 x="1970" y="162"/>
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+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_oxaloacetate_mito3_1" speciesReference="sr_oxaloacetate_mito3_1" speciesGlyph="SpeciesGlyph_oxaloacetate_mito3" role="product">
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+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
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+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_nadh_mito3" speciesReference="sr_nadh_mito3" speciesGlyph="SpeciesGlyph_nadh_mito3" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
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+ </listOfCurveSegments>
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+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_h_mito3" speciesReference="sr_h_mito3" speciesGlyph="SpeciesGlyph_h_mito3" role="product">
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+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
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+ </speciesReferenceGlyph>
+ </listOfSpeciesReferenceGlyphs>
+ </reactionGlyph>
+ <reactionGlyph id="rg_aspartateat_mito3" reaction="reaction_aspartateat_mito3">
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+ </curve>
+ <listOfSpeciesReferenceGlyphs>
+ <speciesReferenceGlyph id="srg_oxaloacetate_mito3_2" speciesReference="sr_oxaloacetate_mito3_2" speciesGlyph="SpeciesGlyph_oxaloacetate_mito3" role="substrate">
+ <curve>
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+ <curveSegment xsi:type="LineSegment">
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+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_glutamate_mito3_1" speciesReference="sr_glutamate_mito3_1" speciesGlyph="SpeciesGlyph_glutamate_mito3" role="substrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
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+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_aspartate_mito3_1" speciesReference="sr_aspartate_mito3_1" speciesGlyph="SpeciesGlyph_aspartate_mito3" role="product">
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+ <curveSegment xsi:type="LineSegment">
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+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_aKetoglutaratemito3_1" speciesReference="sr_aKetoglutarate_mito3_1" speciesGlyph="SpeciesGlyph_aKetoglutarate_mito3" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
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+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ </listOfSpeciesReferenceGlyphs>
+ </reactionGlyph>
+ <reactionGlyph id="rg_aspartateCarrier" reaction="aspartateCarrier">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
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+ <end x="1360" y="550"/>
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+ </listOfCurveSegments>
+ </curve>
+ <listOfSpeciesReferenceGlyphs>
+ <speciesReferenceGlyph id="srg_aspartate_mito3_2" speciesReference="sr_aspartate_mito3_2" speciesGlyph="SpeciesGlyph_aspartate_mito3" role="substrate">
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+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
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+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_aspartate_cyt_2" speciesReference="sr_aspartate_cyt_2" speciesGlyph="SpeciesGlyph_aspartate_cyt" role="product">
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+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
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+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_glutamate_cyt_2" speciesReference="sr_glutamate_cyt_2" speciesGlyph="SpeciesGlyph_glutamate_cyt" role="substrate">
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+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
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+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_glutamate_mito3_2" speciesReference="sr_glutamate_mito3_2" speciesGlyph="SpeciesGlyph_glutamate_mito3" role="product">
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+ <curveSegment xsi:type="CubicBezier">
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+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ </listOfSpeciesReferenceGlyphs>
+ </reactionGlyph>
+ <reactionGlyph id="rg_malateCarrier" reaction="malateCarrier">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
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+ <end x="1360" y="340"/>
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+ </listOfCurveSegments>
+ </curve>
+ <listOfSpeciesReferenceGlyphs>
+ <speciesReferenceGlyph id="srg_aKetoglutarate_mito3_2" speciesReference="sr_aKetoglutarate_mito3_2" speciesGlyph="SpeciesGlyph_aKetoglutarate_mito3" role="substrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
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+ <end x="1530" y="318"/>
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+ </listOfCurveSegments>
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+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_aKetoglutarate_cyt_2" speciesReference="sr_aKetoglutarate_cyt_2" speciesGlyph="SpeciesGlyph_aKetoglutarate_cyt" role="product">
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+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_malate_cyt_2" speciesReference="sr_malate_cyt_2" speciesGlyph="SpeciesGlyph_malate_cyt" role="substrate">
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+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
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+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_malate_mito3_2" speciesReference="sr_malate_mito3_2" speciesGlyph="SpeciesGlyph_malate_mito3" role="product">
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+ <curveSegment xsi:type="CubicBezier">
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+ </speciesReferenceGlyph>
+ </listOfSpeciesReferenceGlyphs>
+ </reactionGlyph>
+ <!--<reactionGlyph id="rg_frame">
+ <boundingBox>
+ <position x="0" y="0"/>
+ <dimensions width="0" height="0"/>
+ </boundingBox>
+ <listOfSpeciesReferenceGlyphs>
+ <speciesReferenceGlyph id="srg_line_1">
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+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
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+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_line_2">
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+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
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+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ </listOfSpeciesReferenceGlyphs>
+ </reactionGlyph> -->
+ </listOfReactionGlyphs>
+ <listOfTextGlyphs>
+ <textGlyph id="TextGlyph_Hepatocyte" graphicalObject="CompartmentGlyph_1" originOfText="Hepatocyte">
+ <boundingBox id="bb_tg_compartment">
+ <position x="50" y="870"/>
+ <dimensions width="300" height="72"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_mito1" graphicalObject="Mito1_Glyph" originOfText="Mito_1">
+ <boundingBox id="bb_tg_mito1">
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+ </textGlyph>
+ <textGlyph id="TextGlyph_mito2" graphicalObject="Mito2_Glyph" originOfText="Mito_2">
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+ <dimensions width="280" height="72"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_mito3" graphicalObject="Mito3_Glyph" originOfText="Mito_3">
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+ <dimensions width="280" height="72"/>
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+ </textGlyph>
+ <textGlyph id="TextGlyph_mito3_2" graphicalObject="Mito3_Glyph_2" originOfText="Mito_3">
+ <boundingBox id="bb_tg_mito3_2">
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+ <dimensions width="200" height="72"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_malate_cyt" graphicalObject="SpeciesGlyph_malate_cyt" originOfText="malate_cyt">
+ <boundingBox id="bb_tg_malatate_cyt">
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+ <dimensions width="220" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_oxaloacetate_cyt" graphicalObject="SpeciesGlyph_oxaloacetate_cyt" originOfText="oxaloacetate_cyt">
+ <boundingBox id="bb_tg_oxaloacetate_cyt">
+ <position x="590" y="480"/>
+ <dimensions width="220" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_aspartate_cyt" graphicalObject="SpeciesGlyph_aspartate_cyt" originOfText="aspartate_cyt">
+ <boundingBox id="bb_tg_aspartate_cyt">
+ <position x="590" y="680"/>
+ <dimensions width="220" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_glutamate_cyt" graphicalObject="SpeciesGlyph_glutamate_cyt" originOfText="glutamate_cyt">
+ <boundingBox id="bb_tg_glutamate_cyt">
+ <position x="810" y="610"/>
+ <dimensions width="220" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_aKetoglutarate_cyt" graphicalObject="SpeciesGlyph_aKetoglutarate_cyt" originOfText="aKetoglutarate_cyt">
+ <boundingBox id="bb_tg_aKetoglutarate_cyt">
+ <position x="870" y="500"/>
+ <dimensions width="260" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_nad_cyt" graphicalObject="SpeciesGlyph_nad_cyt" originOfText="nad_cyt">
+ <boundingBox id="bb_tg_nad_cyt">
+ <position x="525" y="350"/>
+ <dimensions width="80" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_nadh_cyt" graphicalObject="SpeciesGlyph_nadh_cyt" originOfText="nadh_cyt">
+ <boundingBox id="bb_tg_nadh_cyt">
+ <position x="525" y="430"/>
+ <dimensions width="80" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_h_cyt" graphicalObject="SpeciesGlyph_h_cyt" originOfText="h_cyt">
+ <boundingBox id="bb_tg_h_cyt">
+ <position x="435" y="430"/>
+ <dimensions width="30" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="tg_rg_malaltedh_cyt" graphicalObject="rg_malatedh_cyt" originOfText="reaction_malatedh_cyt">
+ <boundingBox id="bb_tg_rg_malaltedh_cyt">
+ <position x="700" y="385"/>
+ <dimensions width="210" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="tg_rg_aspartateat_cyt" graphicalObject="rg_aspartateat_cyt" originOfText="reaction_aspartateat_cyt">
+ <boundingBox id="bb_tg_rg_aspartateat_cyt">
+ <position x="440" y="585"/>
+ <dimensions width="260" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_malate_mito3" graphicalObject="SpeciesGlyph_malate_mito3" originOfText="malate_mito3">
+ <boundingBox id="bb_tg_malatate_mito3">
+ <position x="1860" y="80"/>
+ <dimensions width="220" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_oxaloacetate_mito3" graphicalObject="SpeciesGlyph_oxaloacetate_mito3" originOfText="oxaloacetate_mito3">
+ <boundingBox id="bb_tg_oxaloacetate_mito3">
+ <position x="1860" y="280"/>
+ <dimensions width="220" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_aspartate_mito3" graphicalObject="SpeciesGlyph_aspartate_mito3" originOfText="aspartate_mito3">
+ <boundingBox id="bb_tg_aspartate_mito3">
+ <position x="1860" y="480"/>
+ <dimensions width="220" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_glutamate_mito3" graphicalObject="SpeciesGlyph_glutamate_mito3" originOfText="glutamate_mito3">
+ <boundingBox id="bb_tg_glutamate_mito3">
+ <position x="1560" y="430"/>
+ <dimensions width="220" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_aKetoglutarate_mito3" graphicalObject="SpeciesGlyph_aKetoglutarate_mito3" originOfText="aKetoglutarate_mito3">
+ <boundingBox id="bb_tg_aKetoglutarate_mito3">
+ <position x="1540" y="300"/>
+ <dimensions width="260" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_nad_mito3" graphicalObject="SpeciesGlyph_nad_mito3" originOfText="nad_mito3">
+ <boundingBox id="bb_tg_nad_mito3">
+ <position x="2055" y="150"/>
+ <dimensions width="80" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_nadh_mito3" graphicalObject="SpeciesGlyph_nadh_mito3" originOfText="nadh_mito3">
+ <boundingBox id="bb_tg_nadh_mito3">
+ <position x="2055" y="230"/>
+ <dimensions width="80" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_h_mito3" graphicalObject="SpeciesGlyph_h_mito3" originOfText="h_mito3">
+ <boundingBox id="bb_tg_h_mito3">
+ <position x="2205" y="230"/>
+ <dimensions width="30" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="tg_rg_malatedh_mito3" graphicalObject="rg_malatedh_mito3" originOfText="reaction_malatedh_mito3">
+ <boundingBox id="bb_tg_rg_malatedh_mito3">
+ <position x="1740" y="185"/>
+ <dimensions width="220" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="tg_rg_aspartateat_mito3" graphicalObject="rg_aspartateat_mito3" originOfText="reaction_aspartateat_mito3">
+ <boundingBox id="bb_tg_rg_aspartateat_mito3">
+ <position x="1970" y="385"/>
+ <dimensions width="260" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="tg_rg_aspartateCarrier" graphicalObject="rg_aspartateCarrier" originOfText="aspartateCarrier">
+ <boundingBox id="bb_tg_rg_aspartateCarrier">
+ <position x="1380" y="500"/>
+ <dimensions width="160" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="tg_rg_malateCarrier" graphicalObject="rg_malateCarrier" originOfText="malateCarrier">
+ <boundingBox id="bb_tg_rg_malateCarrier">
+ <position x="1360" y="330"/>
+ <dimensions width="140" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ </listOfTextGlyphs>
+ </layout>
+ </listOfLayouts>
+ </annotation>
+ <listOfCompartments>
+ <compartment id="Hepatocyte" name="Hepatocyte" size="1"/>
+ <compartment id="Mito_1" name="Mito 1" size="1" outside="Hepatocyte"/>
+ <compartment id="Mito_2" name="Mito 2" size="1" outside="Hepatocyte"/>
+ <compartment id="Mito_3" name="Mito 3" size="1" outside="Hepatocyte"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="malate_cyt" name="Malate" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="malate_mito1" name="Malate" compartment="Mito_1" initialConcentration="0"/>
+ <species id="malate_mito2" name="Malate" compartment="Mito_2" initialConcentration="0"/>
+ <species id="malate_mito3" name="Malate" compartment="Mito_3" initialConcentration="0"/>
+ <species id="oxaloacetate_cyt" name="Oxaloacetate" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="oxaloacetate_mito1" name="Oxaloacetate" compartment="Mito_1" initialConcentration="0"/>
+ <species id="oxaloacetate_mito2" name="Oxaloacetate" compartment="Mito_2" initialConcentration="0"/>
+ <species id="oxaloacetate_mito3" name="Oxaloacetate" compartment="Mito_3" initialConcentration="0"/>
+ <species id="aspartate_cyt" name="Aspartate" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="aspartate_mito1" name="Aspartate" compartment="Mito_1" initialConcentration="0"/>
+ <species id="aspartate_mito2" name="Aspartate" compartment="Mito_2" initialConcentration="0"/>
+ <species id="aspartate_mito3" name="Aspartate" compartment="Mito_3" initialConcentration="0"/>
+ <species id="glutamate_cyt" name="Glutamate" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="glutamate_mito1" name="Glutamate" compartment="Mito_1" initialConcentration="0"/>
+ <species id="glutamate_mito2" name="Glutamate" compartment="Mito_2" initialConcentration="0"/>
+ <species id="glutamate_mito3" name="Glutamate" compartment="Mito_3" initialConcentration="0"/>
+ <species id="aKetoglutarate_cyt" name="alpha-Ketoglutarate" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="aKetoglutarate_mito1" name="alpha-Ketoglutarate" compartment="Mito_1" initialConcentration="0"/>
+ <species id="aKetoglutarate_mito2" name="alpha-Ketoglutarate" compartment="Mito_2" initialConcentration="0"/>
+ <species id="aKetoglutarate_mito3" name="alpha-Ketoglutarate" compartment="Mito_3" initialConcentration="0"/>
+ <species id="h_cyt" name="H+" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="h_mito1" name="H+" compartment="Mito_1" initialConcentration="0"/>
+ <species id="h_mito2" name="H+" compartment="Mito_2" initialConcentration="0"/>
+ <species id="h_mito3" name="H+" compartment="Mito_3" initialConcentration="0"/>
+ <species id="nad_cyt" name="NAD+" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="nad_mito1" name="NAD+" compartment="Mito_1" initialConcentration="0"/>
+ <species id="nad_mito2" name="NAD+" compartment="Mito_2" initialConcentration="0"/>
+ <species id="nad_mito3" name="NAD+" compartment="Mito_3" initialConcentration="0"/>
+ <species id="nadh_cyt" name="NADH" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="nadh_mito1" name="NADH" compartment="Mito_1" initialConcentration="0"/>
+ <species id="nadh_mito2" name="NADH" compartment="Mito_2" initialConcentration="0"/>
+ <species id="nadh_mito3" name="NADH" compartment="Mito_3" initialConcentration="0"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="reaction_malatedh_cyt" name="malate dehydrogenase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="malate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_malate_cyt"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="nad_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nad_cyt"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="nadh_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nadh_cyt"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="h_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_h_cyt"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="oxaloacetate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_cyt_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="reaction_aspartateat_cyt" name="aspartate aminotransferase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="oxaloacetate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_cyt_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="glutamate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_glutamate_cyt_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="aspartate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aspartate_cyt_1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="aKetoglutarate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aKetoglutarate_cyt_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="reaction_malatedh_mito1" name="malate dehydrogenase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="malate_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_malate_mito1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="nad_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nad_mito1"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="nadh_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nadh_mito1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="h_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_h_mito1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="oxaloacetate_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_mito1_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="reaction_aspartateat_mito1" name="aspartate aminotransferase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="oxaloacetate_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_mito1_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="glutamate_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_glutamate_mito1"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="aspartate_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aspartate_mito1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="aKetoglutarate_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aKetoglutarate_mito1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="reaction_malatedh_mito2" name="malate dehydrogenase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="malate_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_malate_mito2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="nad_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nad_mito2"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="nadh_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nadh_mito2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="h_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_h_mito2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="oxaloacetate_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_mito2_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="reaction_aspartateat_mito2" name="aspartate aminotransferase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="oxaloacetate_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_mito2_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="glutamate_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_glutamate_mito2"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="aspartate_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aspartate_mito2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="aKetoglutarate_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aKetoglutarate_mito2"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="reaction_malatedh_mito3" name="malate dehydrogenase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="malate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_malate_mito3"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="nad_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nad_mito3"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="nadh_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nadh_mito3"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="h_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_h_mito3"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="oxaloacetate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_mito3_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="reaction_aspartateat_mito3" name="aspartate aminotransferase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="oxaloacetate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_mito3_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="glutamate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_glutamate_mito3_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="aspartate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aspartate_mito3_1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="aKetoglutarate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aKetoglutarate_mito3_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="aspartateCarrier" name="aspartate carrier">
+ <listOfReactants>
+ <speciesReference species="glutamate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_glutamate_mito3_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="aspartate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aspartate_cyt_2"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="glutamate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_glutamate_cyt_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="aspartate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aspartate_mito3_2"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="malateCarrier" name="malate carrier">
+ <listOfReactants>
+ <speciesReference species="aKetoglutarate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aKetoglutarate_mito3_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="malate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_malate_cyt_2"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="aKetoglutarate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aKetoglutarate_cyt_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="malate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_malate_mito3_2"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/converter-sbml/testFiles/layoutExample/example5_level3.xml b/converter-sbml/testFiles/layoutExample/example5_level3.xml
new file mode 100644
index 0000000000000000000000000000000000000000..3cb9bf9885c22453d6bf3218efe717386a634446
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/example5_level3.xml
@@ -0,0 +1,857 @@
+<?xml version='1.0' encoding='utf-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" layout:required="false" level="3" version="1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+ <model areaUnits="area" extentUnits="substance" id="TestModel" lengthUnits="metre" substanceUnits="substance" timeUnits="second" volumeUnits="volume">
+ <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <layout:layout layout:id="Layout_1">
+ <layout:dimensions layout:height="1000" layout:width="2300" />
+ <layout:listOfCompartmentGlyphs>
+ <layout:compartmentGlyph layout:compartment="Hepatocyte" layout:id="CompartmentGlyph_1">
+ <layout:boundingBox layout:id="bb_compartment">
+ <layout:position layout:x="10" layout:y="10" />
+ <layout:dimensions layout:height="980" layout:width="1380" />
+ </layout:boundingBox>
+ </layout:compartmentGlyph>
+ <layout:compartmentGlyph layout:compartment="Mito_1" layout:id="Mito1_Glyph">
+ <layout:boundingBox layout:id="bb_mito1">
+ <layout:position layout:x="100" layout:y="100" />
+ <layout:dimensions layout:height="100" layout:width="300" />
+ </layout:boundingBox>
+ </layout:compartmentGlyph>
+ <layout:compartmentGlyph layout:compartment="Mito_2" layout:id="Mito2_Glyph">
+ <layout:boundingBox layout:id="bb_mito2">
+ <layout:position layout:x="200" layout:y="650" />
+ <layout:dimensions layout:height="100" layout:width="300" />
+ </layout:boundingBox>
+ </layout:compartmentGlyph>
+ <layout:compartmentGlyph layout:compartment="Mito_3" layout:id="Mito3_Glyph">
+ <layout:boundingBox layout:id="bb_mito3">
+ <layout:position layout:x="1000" layout:y="800" />
+ <layout:dimensions layout:height="100" layout:width="300" />
+ </layout:boundingBox>
+ </layout:compartmentGlyph>
+ <layout:compartmentGlyph layout:compartment="Mito_3" layout:id="Mito3_Glyph_2">
+ <layout:boundingBox layout:id="bb_mito3_2">
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+ </layout:speciesReferenceGlyph>
+ </layout:listOfSpeciesReferenceGlyphs>
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+ </layout:listOfReactionGlyphs>
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+ </layout:boundingBox>
+ </layout:textGlyph>
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+ <speciesReference constant="true" id="sr_nad_cyt" species="nad_cyt" stoichiometry="1" />
+ </listOfReactants>
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+ <speciesReference constant="true" id="sr_h_cyt" species="h_cyt" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_oxaloacetate_cyt_1" species="oxaloacetate_cyt" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
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+ <speciesReference constant="true" id="sr_glutamate_cyt_1" species="glutamate_cyt" stoichiometry="1" />
+ </listOfReactants>
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+ <speciesReference constant="true" id="sr_aKetoglutarate_cyt_1" species="aKetoglutarate_cyt" stoichiometry="1" />
+ </listOfProducts>
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+ <speciesReference constant="true" id="sr_nad_mito1" species="nad_mito1" stoichiometry="1" />
+ </listOfReactants>
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+ <speciesReference constant="true" id="sr_oxaloacetate_mito1_1" species="oxaloacetate_mito1" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
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+ <speciesReference constant="true" id="sr_glutamate_mito1" species="glutamate_mito1" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
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+ <speciesReference constant="true" id="sr_aKetoglutarate_mito1" species="aKetoglutarate_mito1" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
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+ <speciesReference constant="true" id="sr_nad_mito2" species="nad_mito2" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
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+ <speciesReference constant="true" id="sr_h_mito2" species="h_mito2" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_oxaloacetate_mito2_1" species="oxaloacetate_mito2" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="reaction_aspartateat_mito2" name="aspartate aminotransferase" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="sr_oxaloacetate_mito2_2" species="oxaloacetate_mito2" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_glutamate_mito2" species="glutamate_mito2" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="sr_aspartate_mito2" species="aspartate_mito2" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_aKetoglutarate_mito2" species="aKetoglutarate_mito2" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="reaction_malatedh_mito3" name="malate dehydrogenase" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="sr_malate_mito3" species="malate_mito3" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_nad_mito3" species="nad_mito3" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="sr_nadh_mito3" species="nadh_mito3" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_h_mito3" species="h_mito3" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_oxaloacetate_mito3_1" species="oxaloacetate_mito3" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="reaction_aspartateat_mito3" name="aspartate aminotransferase" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="sr_oxaloacetate_mito3_2" species="oxaloacetate_mito3" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_glutamate_mito3_1" species="glutamate_mito3" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="sr_aspartate_mito3_1" species="aspartate_mito3" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_aKetoglutarate_mito3_1" species="aKetoglutarate_mito3" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="aspartateCarrier" name="aspartate carrier" reversible="true">
+ <listOfReactants>
+ <speciesReference constant="true" id="sr_glutamate_mito3_2" species="glutamate_mito3" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_aspartate_cyt_2" species="aspartate_cyt" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="sr_glutamate_cyt_2" species="glutamate_cyt" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_aspartate_mito3_2" species="aspartate_mito3" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="malateCarrier" name="malate carrier" reversible="true">
+ <listOfReactants>
+ <speciesReference constant="true" id="sr_aKetoglutarate_mito3_2" species="aKetoglutarate_mito3" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_malate_cyt_2" species="malate_cyt" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="sr_aKetoglutarate_cyt_2" species="aKetoglutarate_cyt" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_malate_mito3_2" species="malate_mito3" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/converter-sbml/testFiles/layoutExample/example6.xml b/converter-sbml/testFiles/layoutExample/example6.xml
new file mode 100644
index 0000000000000000000000000000000000000000..4ec944bf0bcfc218663dde0f9e972cad4f52d33a
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/example6.xml
@@ -0,0 +1,980 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+ <model id="TestModel">
+ <annotation>
+ <listOfLayouts xmlns="http://projects.eml.org/bcb/sbml/level2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <layout id="Layout_1">
+ <dimensions width="2320" height="1000"/>
+ <listOfCompartmentGlyphs>
+ <compartmentGlyph id="CompartmentGlyph_1" compartment="Hepatocyte">
+ <boundingBox id="bb_compartment">
+ <position x="10" y="10"/>
+ <dimensions width="2300" height="980"/>
+ </boundingBox>
+ </compartmentGlyph>
+ <compartmentGlyph id="Mito1_Glyph" compartment="Mito_1">
+ <boundingBox id="bb_mito1">
+ <position x="100" y="100"/>
+ <dimensions width="300" height="100"/>
+ </boundingBox>
+ </compartmentGlyph>
+ <compartmentGlyph id="Mito2_Glyph" compartment="Mito_2">
+ <boundingBox id="bb_mito2">
+ <position x="200" y="650"/>
+ <dimensions width="300" height="100"/>
+ </boundingBox>
+ </compartmentGlyph>
+ <compartmentGlyph id="Mito3_Glyph_2" compartment="Mito_3">
+ <boundingBox id="bb_mito3_2">
+ <position x="1470" y="30"/>
+ <dimensions width="820" height="536"/>
+ </boundingBox>
+ </compartmentGlyph>
+ </listOfCompartmentGlyphs>
+ <listOfSpeciesGlyphs>
+ <speciesGlyph id="SpeciesGlyph_malate_cyt" species="malate_cyt">
+ <boundingBox id="bb_sg_malate_cyt">
+ <position x="580" y="280"/>
+ <dimensions width="240" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_oxaloacetate_cyt" species="oxaloacetate_cyt">
+ <boundingBox id="bb_sg_oxaloacetate_cyt">
+ <position x="580" y="480"/>
+ <dimensions width="240" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_aspartate_cyt" species="aspartate_cyt">
+ <boundingBox id="bb_sg_aspartate_cyt">
+ <position x="580" y="680"/>
+ <dimensions width="240" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_glutamate_cyt" species="glutamate_cyt">
+ <boundingBox id="bb_sg_glutamate_cyt">
+ <position x="800" y="610"/>
+ <dimensions width="240" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_aKetoglutarate_cyt" species="aKetoglutarate_cyt">
+ <boundingBox id="bb_sg_aKetoglutarate_cyt">
+ <position x="860" y="500"/>
+ <dimensions width="280" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_nad_cyt" species="nad_cyt">
+ <boundingBox id="bb_sg_nad_cyt">
+ <position x="520" y="350"/>
+ <dimensions width="100" height="24"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_nadh_cyt" species="nadh_cyt">
+ <boundingBox id="bb_sg_nadh_cyt">
+ <position x="520" y="430"/>
+ <dimensions width="100" height="24"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_h_cyt" species="h_cyt">
+ <boundingBox id="bb_sg_h_cyt">
+ <position x="430" y="430"/>
+ <dimensions width="40" height="24"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_malate_mito3" species="malate_mito3">
+ <boundingBox id="bb_sg_malate_mito3">
+ <position x="1850" y="80"/>
+ <dimensions width="240" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_oxaloacetate_mito3" species="oxaloacetate_mito3">
+ <boundingBox id="bb_sg_oxaloacetate_mito3">
+ <position x="1850" y="280"/>
+ <dimensions width="240" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_aspartate_mito3" species="aspartate_mito3">
+ <boundingBox id="bb_sg_aspartate_mito3">
+ <position x="1850" y="480"/>
+ <dimensions width="240" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_glutamate_mito3" species="glutamate_mito3">
+ <boundingBox id="bb_sg_glutamate_mito3">
+ <position x="1550" y="430"/>
+ <dimensions width="240" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_aKetoglutarate_mito3" species="aKetoglutarate_mito3">
+ <boundingBox id="bb_sg_aKetoglutarate_mito3">
+ <position x="1530" y="300"/>
+ <dimensions width="280" height="36"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_nad_mito3" species="nad_mito3">
+ <boundingBox id="bb_sg_nad_mito3">
+ <position x="2050" y="150"/>
+ <dimensions width="100" height="24"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_nadh_mito3" species="nadh_mito3">
+ <boundingBox id="bb_sg_nadh_mito3">
+ <position x="2050" y="230"/>
+ <dimensions width="100" height="24"/>
+ </boundingBox>
+ </speciesGlyph>
+ <speciesGlyph id="SpeciesGlyph_h_mito3" species="h_mito3">
+ <boundingBox id="bb_sg_h_mito3">
+ <position x="2200" y="230"/>
+ <dimensions width="40" height="24"/>
+ </boundingBox>
+ </speciesGlyph>
+ </listOfSpeciesGlyphs>
+ <listOfReactionGlyphs>
+ <reactionGlyph id="rg_malatedh_cyt" reaction="reaction_malatedh_cyt">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
+ <start x="700" y="381"/>
+ <end x="700" y="415"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ <listOfSpeciesReferenceGlyphs>
+ <speciesReferenceGlyph id="srg_malate_cyt_1" speciesReference="sr_malate_cyt" speciesGlyph="SpeciesGlyph_malate_cyt" role="substrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
+ <start x="700" y="381"/>
+ <end x="700" y="316"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_nad_cyt" speciesReference="sr_nad_cyt" speciesGlyph="SpeciesGlyph_nad_cyt" role="substrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
+ <start x="700" y="381"/>
+ <end x="620" y="362"/>
+ <basePoint1 x="700" y="362"/>
+ <basePoint2 x="700" y="362"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_oxaloacetate_cyt_1" speciesReference="sr_oxaloacetate_cyt_1" speciesGlyph="SpeciesGlyph_oxaloacetate_cyt" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
+ <start x="700" y="415"/>
+ <end x="700" y="480"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_nadh_cyt" speciesReference="sr_nadh_cyt" speciesGlyph="SpeciesGlyph_nadh_cyt" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
+ <start x="700" y="415"/>
+ <end x="620" y="442"/>
+ <basePoint1 x="700" y="442"/>
+ <basePoint2 x="700" y="442"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_h_cyt" speciesReference="sr_h_cyt" speciesGlyph="SpeciesGlyph_h_cyt" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
+ <start x="700" y="415"/>
+ <end x="470" y="430"/>
+ <basePoint1 x="570" y="415"/>
+ <basePoint2 x="570" y="415"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ </listOfSpeciesReferenceGlyphs>
+ </reactionGlyph>
+ <reactionGlyph id="rg_aspartateat_cyt" reaction="reaction_aspartateat_cyt">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
+ <start x="700" y="581"/>
+ <end x="700" y="615"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ <listOfSpeciesReferenceGlyphs>
+ <speciesReferenceGlyph id="srg_oxaloacetate_cyt_2" speciesReference="sr_oxaloacetate_cyt_2" speciesGlyph="SpeciesGlyph_oxaloacetate_cyt" role="substrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
+ <start x="700" y="581"/>
+ <end x="700" y="516"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_glutamate_cyt_1" speciesReference="sr_glutamate_cyt_1" speciesGlyph="SpeciesGlyph_glutamate_cyt" role="substrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
+ <start x="700" y="581"/>
+ <end x="800" y="628"/>
+ <basePoint1 x="750" y="581"/>
+ <basePoint2 x="750" y="628"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_aspartate_cyt_1" speciesReference="sr_aspartate_cyt_1" speciesGlyph="SpeciesGlyph_aspartate_cyt" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
+ <start x="700" y="615"/>
+ <end x="700" y="680"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_aKetoglutaratecyt_1" speciesReference="sr_aKetoglutarate_cyt_1" speciesGlyph="SpeciesGlyph_aKetoglutarate_cyt" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
+ <start x="700" y="615"/>
+ <end x="860" y="515"/>
+ <basePoint1 x="790" y="615"/>
+ <basePoint2 x="790" y="515"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ </listOfSpeciesReferenceGlyphs>
+ </reactionGlyph>
+ <reactionGlyph id="rg_malatedh_mito3" reaction="reaction_malatedh_mito3">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
+ <start x="1970" y="181"/>
+ <end x="1970" y="215"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ <listOfSpeciesReferenceGlyphs>
+ <speciesReferenceGlyph id="srg_malate_mito3_1" speciesReference="sr_malate_mito3" speciesGlyph="SpeciesGlyph_malate_mito3" role="substrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
+ <start x="1970" y="181"/>
+ <end x="1970" y="116"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_nad_mito3" speciesReference="sr_nad_mito3" speciesGlyph="SpeciesGlyph_nad_mito3" role="substrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
+ <start x="1970" y="181"/>
+ <end x="2050" y="162"/>
+ <basePoint1 x="1970" y="162"/>
+ <basePoint2 x="1970" y="162"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_oxaloacetate_mito3_1" speciesReference="sr_oxaloacetate_mito3_1" speciesGlyph="SpeciesGlyph_oxaloacetate_mito3" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
+ <start x="1970" y="215"/>
+ <end x="1970" y="280"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_nadh_mito3" speciesReference="sr_nadh_mito3" speciesGlyph="SpeciesGlyph_nadh_mito3" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
+ <start x="1970" y="215"/>
+ <end x="2050" y="242"/>
+ <basePoint1 x="1970" y="242"/>
+ <basePoint2 x="1970" y="242"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_h_mito3" speciesReference="sr_h_mito3" speciesGlyph="SpeciesGlyph_h_mito3" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
+ <start x="1970" y="215"/>
+ <end x="2200" y="230"/>
+ <basePoint1 x="2100" y="215"/>
+ <basePoint2 x="2100" y="215"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ </listOfSpeciesReferenceGlyphs>
+ </reactionGlyph>
+ <reactionGlyph id="rg_aspartateat_mito3" reaction="reaction_aspartateat_mito3">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
+ <start x="1970" y="381"/>
+ <end x="1970" y="415"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ <listOfSpeciesReferenceGlyphs>
+ <speciesReferenceGlyph id="srg_oxaloacetate_mito3_2" speciesReference="sr_oxaloacetate_mito3_2" speciesGlyph="SpeciesGlyph_oxaloacetate_mito3" role="substrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
+ <start x="1970" y="381"/>
+ <end x="1970" y="316"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_glutamate_mito3_1" speciesReference="sr_glutamate_mito3_1" speciesGlyph="SpeciesGlyph_glutamate_mito3" role="substrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
+ <start x="1970" y="381"/>
+ <end x="1790" y="448"/>
+ <basePoint1 x="1880" y="381"/>
+ <basePoint2 x="1880" y="448"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_aspartate_mito3_1" speciesReference="sr_aspartate_mito3_1" speciesGlyph="SpeciesGlyph_aspartate_mito3" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
+ <start x="1970" y="415"/>
+ <end x="1970" y="480"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_aKetoglutaratemito3_1" speciesReference="sr_aKetoglutarate_mito3_1" speciesGlyph="SpeciesGlyph_aKetoglutarate_mito3" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
+ <start x="1970" y="415"/>
+ <end x="1810" y="315"/>
+ <basePoint1 x="1880" y="415"/>
+ <basePoint2 x="1880" y="315"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ </listOfSpeciesReferenceGlyphs>
+ </reactionGlyph>
+ <reactionGlyph id="rg_aspartateCarrier" reaction="aspartateCarrier">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
+ <start x="1420" y="530"/>
+ <end x="1360" y="550"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ <listOfSpeciesReferenceGlyphs>
+ <speciesReferenceGlyph id="srg_aspartate_mito3_2" speciesReference="sr_aspartate_mito3_2" speciesGlyph="SpeciesGlyph_aspartate_mito3" role="substrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
+ <start x="1420" y="530"/>
+ <end x="1850" y="498"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_aspartate_cyt_2" speciesReference="sr_aspartate_cyt_2" speciesGlyph="SpeciesGlyph_aspartate_cyt" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
+ <start x="1360" y="550"/>
+ <end x="820" y="698"/>
+ <basePoint1 x="1390" y="698"/>
+ <basePoint2 x="1390" y="698"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_glutamate_cyt_2" speciesReference="sr_glutamate_cyt_2" speciesGlyph="SpeciesGlyph_glutamate_cyt" role="substrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
+ <start x="1420" y="530"/>
+ <end x="1050" y="628"/>
+ <basePoint1 x="1390" y="648"/>
+ <basePoint2 x="1390" y="648"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_glutamate_mito3_2" speciesReference="sr_glutamate_mito3_2" speciesGlyph="SpeciesGlyph_glutamate_mito3" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
+ <start x="1360" y="550"/>
+ <end x="1550" y="448"/>
+ <basePoint1 x="1390" y="448"/>
+ <basePoint2 x="1390" y="448"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ </listOfSpeciesReferenceGlyphs>
+ </reactionGlyph>
+ <reactionGlyph id="rg_malateCarrier" reaction="malateCarrier">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
+ <start x="1420" y="320"/>
+ <end x="1360" y="340"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ <listOfSpeciesReferenceGlyphs>
+ <speciesReferenceGlyph id="srg_aKetoglutarate_mito3_2" speciesReference="sr_aKetoglutarate_mito3_2" speciesGlyph="SpeciesGlyph_aKetoglutarate_mito3" role="substrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
+ <start x="1420" y="320"/>
+ <end x="1530" y="318"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_aKetoglutarate_cyt_2" speciesReference="sr_aKetoglutarate_cyt_2" speciesGlyph="SpeciesGlyph_aKetoglutarate_cyt" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="LineSegment">
+ <start x="1360" y="340"/>
+ <end x="1140" y="518"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_malate_cyt_2" speciesReference="sr_malate_cyt_2" speciesGlyph="SpeciesGlyph_malate_cyt" role="substrate">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
+ <start x="1420" y="320"/>
+ <end x="820" y="298"/>
+ <basePoint1 x="1390" y="250"/>
+ <basePoint2 x="1390" y="250"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ <speciesReferenceGlyph id="srg_malate_mito3_2" speciesReference="sr_malate_mito3_2" speciesGlyph="SpeciesGlyph_malate_mito3" role="product">
+ <curve>
+ <listOfCurveSegments>
+ <curveSegment xsi:type="CubicBezier">
+ <start x="1360" y="340"/>
+ <end x="1850" y="98"/>
+ <basePoint1 x="1390" y="150"/>
+ <basePoint2 x="1390" y="150"/>
+ </curveSegment>
+ </listOfCurveSegments>
+ </curve>
+ </speciesReferenceGlyph>
+ </listOfSpeciesReferenceGlyphs>
+ </reactionGlyph>
+ </listOfReactionGlyphs>
+ <listOfTextGlyphs>
+ <textGlyph id="TextGlyph_Hepatocyte" graphicalObject="CompartmentGlyph_1" originOfText="Hepatocyte">
+ <boundingBox id="bb_tg_compartment">
+ <position x="50" y="870"/>
+ <dimensions width="300" height="72"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_mito1" graphicalObject="Mito1_Glyph" originOfText="Mito_1">
+ <boundingBox id="bb_tg_mito1">
+ <position x="110" y="110"/>
+ <dimensions width="280" height="72"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_mito2" graphicalObject="Mito2_Glyph" originOfText="Mito_2">
+ <boundingBox id="bb_tg_mito2">
+ <position x="210" y="660"/>
+ <dimensions width="280" height="72"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_mito3_2" graphicalObject="Mito3_Glyph_2" originOfText="Mito_3">
+ <boundingBox id="bb_tg_mito3_2">
+ <position x="1475" y="35"/>
+ <dimensions width="200" height="72"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_malate_cyt" graphicalObject="SpeciesGlyph_malate_cyt" originOfText="malate_cyt">
+ <boundingBox id="bb_tg_malatate_cyt">
+ <position x="590" y="280"/>
+ <dimensions width="220" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_oxaloacetate_cyt" graphicalObject="SpeciesGlyph_oxaloacetate_cyt" originOfText="oxaloacetate_cyt">
+ <boundingBox id="bb_tg_oxaloacetate_cyt">
+ <position x="590" y="480"/>
+ <dimensions width="220" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_aspartate_cyt" graphicalObject="SpeciesGlyph_aspartate_cyt" originOfText="aspartate_cyt">
+ <boundingBox id="bb_tg_aspartate_cyt">
+ <position x="590" y="680"/>
+ <dimensions width="220" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_glutamate_cyt" graphicalObject="SpeciesGlyph_glutamate_cyt" originOfText="glutamate_cyt">
+ <boundingBox id="bb_tg_glutamate_cyt">
+ <position x="810" y="610"/>
+ <dimensions width="220" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_aKetoglutarate_cyt" graphicalObject="SpeciesGlyph_aKetoglutarate_cyt" originOfText="aKetoglutarate_cyt">
+ <boundingBox id="bb_tg_aKetoglutarate_cyt">
+ <position x="870" y="500"/>
+ <dimensions width="260" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_nad_cyt" graphicalObject="SpeciesGlyph_nad_cyt" originOfText="nad_cyt">
+ <boundingBox id="bb_tg_nad_cyt">
+ <position x="525" y="350"/>
+ <dimensions width="80" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_nadh_cyt" graphicalObject="SpeciesGlyph_nadh_cyt" originOfText="nadh_cyt">
+ <boundingBox id="bb_tg_nadh_cyt">
+ <position x="525" y="430"/>
+ <dimensions width="80" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_h_cyt" graphicalObject="SpeciesGlyph_h_cyt" originOfText="h_cyt">
+ <boundingBox id="bb_tg_h_cyt">
+ <position x="435" y="430"/>
+ <dimensions width="30" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="tg_rg_malaltedh_cyt" graphicalObject="rg_malatedh_cyt" originOfText="reaction_malatedh_cyt">
+ <boundingBox id="bb_tg_rg_malaltedh_cyt">
+ <position x="700" y="385"/>
+ <dimensions width="210" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="tg_rg_aspartateat_cyt" graphicalObject="rg_aspartateat_cyt" originOfText="reaction_aspartateat_cyt">
+ <boundingBox id="bb_tg_rg_aspartateat_cyt">
+ <position x="440" y="585"/>
+ <dimensions width="260" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_malate_mito3" graphicalObject="SpeciesGlyph_malate_mito3" originOfText="malate_mito3">
+ <boundingBox id="bb_tg_malatate_mito3">
+ <position x="1860" y="80"/>
+ <dimensions width="220" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_oxaloacetate_mito3" graphicalObject="SpeciesGlyph_oxaloacetate_mito3" originOfText="oxaloacetate_mito3">
+ <boundingBox id="bb_tg_oxaloacetate_mito3">
+ <position x="1860" y="280"/>
+ <dimensions width="220" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_aspartate_mito3" graphicalObject="SpeciesGlyph_aspartate_mito3" originOfText="aspartate_mito3">
+ <boundingBox id="bb_tg_aspartate_mito3">
+ <position x="1860" y="480"/>
+ <dimensions width="220" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_glutamate_mito3" graphicalObject="SpeciesGlyph_glutamate_mito3" originOfText="glutamate_mito3">
+ <boundingBox id="bb_tg_glutamate_mito3">
+ <position x="1560" y="430"/>
+ <dimensions width="220" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_aKetoglutarate_mito3" graphicalObject="SpeciesGlyph_aKetoglutarate_mito3" originOfText="aKetoglutarate_mito3">
+ <boundingBox id="bb_tg_aKetoglutarate_mito3">
+ <position x="1540" y="300"/>
+ <dimensions width="260" height="36"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_nad_mito3" graphicalObject="SpeciesGlyph_nad_mito3" originOfText="nad_mito3">
+ <boundingBox id="bb_tg_nad_mito3">
+ <position x="2055" y="150"/>
+ <dimensions width="80" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_nadh_mito3" graphicalObject="SpeciesGlyph_nadh_mito3" originOfText="nadh_mito3">
+ <boundingBox id="bb_tg_nadh_mito3">
+ <position x="2055" y="230"/>
+ <dimensions width="80" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="TextGlyph_h_mito3" graphicalObject="SpeciesGlyph_h_mito3" originOfText="h_mito3">
+ <boundingBox id="bb_tg_h_mito3">
+ <position x="2205" y="230"/>
+ <dimensions width="30" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="tg_rg_malatedh_mito3" graphicalObject="rg_malatedh_mito3" originOfText="reaction_malatedh_mito3">
+ <boundingBox id="bb_tg_rg_malatedh_mito3">
+ <position x="1740" y="185"/>
+ <dimensions width="220" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="tg_rg_aspartateat_mito3" graphicalObject="rg_aspartateat_mito3" originOfText="reaction_aspartateat_mito3">
+ <boundingBox id="bb_tg_rg_aspartateat_mito3">
+ <position x="1970" y="385"/>
+ <dimensions width="260" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="tg_rg_aspartateCarrier" graphicalObject="rg_aspartateCarrier" originOfText="aspartateCarrier">
+ <boundingBox id="bb_tg_rg_aspartateCarrier">
+ <position x="1380" y="500"/>
+ <dimensions width="160" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ <textGlyph id="tg_rg_malateCarrier" graphicalObject="rg_malateCarrier" originOfText="malateCarrier">
+ <boundingBox id="bb_tg_rg_malateCarrier">
+ <position x="1360" y="330"/>
+ <dimensions width="140" height="24"/>
+ </boundingBox>
+ </textGlyph>
+ </listOfTextGlyphs>
+ </layout>
+ </listOfLayouts>
+ </annotation>
+ <listOfCompartments>
+ <compartment id="Hepatocyte" name="Hepatocyte" size="1"/>
+ <compartment id="Mito_1" name="Mito 1" size="1" outside="Hepatocyte"/>
+ <compartment id="Mito_2" name="Mito 2" size="1" outside="Hepatocyte"/>
+ <compartment id="Mito_3" name="Mito 3" size="1" outside="Hepatocyte"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="malate_cyt" name="Malate" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="malate_mito1" name="Malate" compartment="Mito_1" initialConcentration="0"/>
+ <species id="malate_mito2" name="Malate" compartment="Mito_2" initialConcentration="0"/>
+ <species id="malate_mito3" name="Malate" compartment="Mito_3" initialConcentration="0"/>
+ <species id="oxaloacetate_cyt" name="Oxaloacetate" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="oxaloacetate_mito1" name="Oxaloacetate" compartment="Mito_1" initialConcentration="0"/>
+ <species id="oxaloacetate_mito2" name="Oxaloacetate" compartment="Mito_2" initialConcentration="0"/>
+ <species id="oxaloacetate_mito3" name="Oxaloacetate" compartment="Mito_3" initialConcentration="0"/>
+ <species id="aspartate_cyt" name="Aspartate" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="aspartate_mito1" name="Aspartate" compartment="Mito_1" initialConcentration="0"/>
+ <species id="aspartate_mito2" name="Aspartate" compartment="Mito_2" initialConcentration="0"/>
+ <species id="aspartate_mito3" name="Aspartate" compartment="Mito_3" initialConcentration="0"/>
+ <species id="glutamate_cyt" name="Glutamate" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="glutamate_mito1" name="Glutamate" compartment="Mito_1" initialConcentration="0"/>
+ <species id="glutamate_mito2" name="Glutamate" compartment="Mito_2" initialConcentration="0"/>
+ <species id="glutamate_mito3" name="Glutamate" compartment="Mito_3" initialConcentration="0"/>
+ <species id="aKetoglutarate_cyt" name="alpha-Ketoglutarate" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="aKetoglutarate_mito1" name="alpha-Ketoglutarate" compartment="Mito_1" initialConcentration="0"/>
+ <species id="aKetoglutarate_mito2" name="alpha-Ketoglutarate" compartment="Mito_2" initialConcentration="0"/>
+ <species id="aKetoglutarate_mito3" name="alpha-Ketoglutarate" compartment="Mito_3" initialConcentration="0"/>
+ <species id="h_cyt" name="H+" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="h_mito1" name="H+" compartment="Mito_1" initialConcentration="0"/>
+ <species id="h_mito2" name="H+" compartment="Mito_2" initialConcentration="0"/>
+ <species id="h_mito3" name="H+" compartment="Mito_3" initialConcentration="0"/>
+ <species id="nad_cyt" name="NAD+" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="nad_mito1" name="NAD+" compartment="Mito_1" initialConcentration="0"/>
+ <species id="nad_mito2" name="NAD+" compartment="Mito_2" initialConcentration="0"/>
+ <species id="nad_mito3" name="NAD+" compartment="Mito_3" initialConcentration="0"/>
+ <species id="nadh_cyt" name="NADH" compartment="Hepatocyte" initialConcentration="0"/>
+ <species id="nadh_mito1" name="NADH" compartment="Mito_1" initialConcentration="0"/>
+ <species id="nadh_mito2" name="NADH" compartment="Mito_2" initialConcentration="0"/>
+ <species id="nadh_mito3" name="NADH" compartment="Mito_3" initialConcentration="0"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="reaction_malatedh_cyt" name="malate dehydrogenase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="malate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_malate_cyt"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="nad_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nad_cyt"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="nadh_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nadh_cyt"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="h_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_h_cyt"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="oxaloacetate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_cyt_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="reaction_aspartateat_cyt" name="aspartate aminotransferase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="oxaloacetate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_cyt_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="glutamate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_glutamate_cyt_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="aspartate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aspartate_cyt_1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="aKetoglutarate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aKetoglutarate_cyt_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="reaction_malatedh_mito1" name="malate dehydrogenase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="malate_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_malate_mito1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="nad_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nad_mito1"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="nadh_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nadh_mito1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="h_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_h_mito1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="oxaloacetate_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_mito1_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="reaction_aspartateat_mito1" name="aspartate aminotransferase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="oxaloacetate_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_mito1_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="glutamate_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_glutamate_mito1"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="aspartate_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aspartate_mito1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="aKetoglutarate_mito1">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aKetoglutarate_mito1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="reaction_malatedh_mito2" name="malate dehydrogenase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="malate_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_malate_mito2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="nad_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nad_mito2"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="nadh_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nadh_mito2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="h_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_h_mito2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="oxaloacetate_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_mito2_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="reaction_aspartateat_mito2" name="aspartate aminotransferase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="oxaloacetate_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_mito2_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="glutamate_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_glutamate_mito2"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="aspartate_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aspartate_mito2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="aKetoglutarate_mito2">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aKetoglutarate_mito2"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="reaction_malatedh_mito3" name="malate dehydrogenase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="malate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_malate_mito3"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="nad_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nad_mito3"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="nadh_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_nadh_mito3"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="h_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_h_mito3"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="oxaloacetate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_mito3_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="reaction_aspartateat_mito3" name="aspartate aminotransferase" reversible="false">
+ <listOfReactants>
+ <speciesReference species="oxaloacetate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_oxaloacetate_mito3_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="glutamate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_glutamate_mito3_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="aspartate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aspartate_mito3_1"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="aKetoglutarate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aKetoglutarate_mito3_1"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="aspartateCarrier" name="aspartate carrier">
+ <listOfReactants>
+ <speciesReference species="glutamate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_glutamate_mito3_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="aspartate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aspartate_cyt_2"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="glutamate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_glutamate_cyt_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="aspartate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aspartate_mito3_2"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ <reaction id="malateCarrier" name="malate carrier">
+ <listOfReactants>
+ <speciesReference species="aKetoglutarate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aKetoglutarate_mito3_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="malate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_malate_cyt_2"/>
+ </annotation>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="aKetoglutarate_cyt">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_aKetoglutarate_cyt_2"/>
+ </annotation>
+ </speciesReference>
+ <speciesReference species="malate_mito3">
+ <annotation>
+ <layoutId xmlns="http://projects.eml.org/bcb/sbml/level2" id="sr_malate_mito3_2"/>
+ </annotation>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/converter-sbml/testFiles/layoutExample/example6_level3.xml b/converter-sbml/testFiles/layoutExample/example6_level3.xml
new file mode 100644
index 0000000000000000000000000000000000000000..b2f31da59ba89130835b04f68b08864aa3749690
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/example6_level3.xml
@@ -0,0 +1,845 @@
+<?xml version='1.0' encoding='utf-8' standalone='no'?>
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+ <listOfReactants>
+ <speciesReference constant="true" id="sr_malate_mito2" species="malate_mito2" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_nad_mito2" species="nad_mito2" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="sr_nadh_mito2" species="nadh_mito2" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_h_mito2" species="h_mito2" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_oxaloacetate_mito2_1" species="oxaloacetate_mito2" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="reaction_aspartateat_mito2" name="aspartate aminotransferase" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="sr_oxaloacetate_mito2_2" species="oxaloacetate_mito2" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_glutamate_mito2" species="glutamate_mito2" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="sr_aspartate_mito2" species="aspartate_mito2" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_aKetoglutarate_mito2" species="aKetoglutarate_mito2" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="reaction_malatedh_mito3" name="malate dehydrogenase" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="sr_malate_mito3" species="malate_mito3" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_nad_mito3" species="nad_mito3" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="sr_nadh_mito3" species="nadh_mito3" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_h_mito3" species="h_mito3" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_oxaloacetate_mito3_1" species="oxaloacetate_mito3" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="reaction_aspartateat_mito3" name="aspartate aminotransferase" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" id="sr_oxaloacetate_mito3_2" species="oxaloacetate_mito3" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_glutamate_mito3_1" species="glutamate_mito3" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="sr_aspartate_mito3_1" species="aspartate_mito3" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_aKetoglutarate_mito3_1" species="aKetoglutarate_mito3" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="aspartateCarrier" name="aspartate carrier" reversible="true">
+ <listOfReactants>
+ <speciesReference constant="true" id="sr_glutamate_mito3_2" species="glutamate_mito3" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_aspartate_cyt_2" species="aspartate_cyt" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="sr_glutamate_cyt_2" species="glutamate_cyt" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_aspartate_mito3_2" species="aspartate_mito3" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="malateCarrier" name="malate carrier" reversible="true">
+ <listOfReactants>
+ <speciesReference constant="true" id="sr_aKetoglutarate_mito3_2" species="aKetoglutarate_mito3" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_malate_cyt_2" species="malate_cyt" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" id="sr_aKetoglutarate_cyt_2" species="aKetoglutarate_cyt" stoichiometry="1" />
+ <speciesReference constant="true" id="sr_malate_mito3_2" species="malate_mito3" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/pom.xml b/pom.xml
index 6da6fa5d7c9371f53a610c110362519bd0d1d82c..be583c05b21d751798a01048bf847c29d2a6e06f 100644
--- a/pom.xml
+++ b/pom.xml
@@ -118,6 +118,7 @@
<module>editor</module>
<module>rest-api</module>
<module>frontend-js</module>
+ <module>converter-sbml</module>
</modules>
<build>